Entry - *300013 - N-ALPHA-ACETYLTRANSFERASE 10, NatA CATALYTIC SUBUNIT; NAA10 - OMIM
* 300013

N-ALPHA-ACETYLTRANSFERASE 10, NatA CATALYTIC SUBUNIT; NAA10


Alternative titles; symbols

ARD1 N-ACETYLTRANSFERASE, S. CEREVISIAE, HOMOLOG OF, A; ARD1A
ARREST-DEFECTIVE PROTEIN 1; ARD1
TE2


HGNC Approved Gene Symbol: NAA10

Cytogenetic location: Xq28   Genomic coordinates (GRCh38) : X:153,929,225-153,935,037 (from NCBI)


Gene-Phenotype Relationships
Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
Xq28 Microphthalmia, syndromic 1 309800 XL 3
Ogden syndrome 300855 XLD, XLR 3

TEXT

Description

N-alpha-acetylation is a common protein modification that occurs during protein synthesis and involves the transfer of an acetyl group from acetyl-coenzyme A to the protein alpha-amino group. ARD1A, together with NATH (NARG1, NAA15; 608000), is part of a major N-alpha-acetyltransferase complex responsible for alpha-acetylation of proteins and peptides (Sanchez-Puig and Fersht, 2006).


Cloning and Expression

Tribioli et al. (1994) described the physical and transcriptional organization of a region of 140 kb in Xq28, 5-prime to the L1CAM gene (308840). They established a transcriptional map of the region by isolating and mapping CpG islands to the physical map, determining partial nucleotide sequences, and studying the pattern of expression and orientation of the transcripts. They succeeded in positioning 4 previously identified genes: L1CAM, AVPR2 (300538), HFC1 (300019), and RENBP (312420). All genes in the region are rather small, ranging in size from 2 to 30 kb, and very close to one another. With the exception of the AVPR2 gene, they serve a housekeeping function, having a CpG island at their 5-prime end and the same orientation of transcription. This kind of organization is consistent with the one previously described for the more distal portion of Xq28, between the color vision pigment genes and the G6PD gene and indicates that genes with a housekeeping and tissue-specific pattern of expression are interspersed in the genome but are probably found in different 'transcriptional domains' (characterized by different orientation). Three new genes were identified and positioned. One of these, termed TE2, demonstrated 40% identity with the ARD1 protein of Saccharomyces cerevisiae (Whiteway and Szostak, 1985), a protein required for the expression of an N-terminal protein acetyltransferase activity.

Using Northern blot analysis, Sugiura et al. (2003) showed mouse Ard1 was ubiquitously expressed. By database analysis and PCR, Kim et al. (2006) identified 3 splice variants of mouse Ard1 and 2 splice variants of human ARD1. The mouse variants encoded proteins of 235-, 225-, and 198-amino acids. Ard1(235) and Ard1(225) have well-conserved N-acetyltransferase domains, but Ard1(198) has only a partial domain. The human ARD1 variants encoded proteins of 131- and 235-amino acids. The C-terminal region of mouse Ard1(225) differs from that of both mouse and human ARD1(235), likely due to alternative splicing of exon 8. Western blot analysis of human cell lines showed a major intense band of about 32 kD, which corresponded to ARD1(235). In contrast, mouse fibroblasts strongly expressed a 30-kD protein, corresponding to Ard1(225).

Asaumi et al. (2005) cloned ARD1 and identified it as a potential APP (104760)-binding protein in a yeast 2-hybrid assay. The 235-amino acid protein contains an N-acetyltransferase domain, a highly conserved acetyl-coenzyme A binding motif, and a C-terminal APP-binding domain.


Gene Structure

Popp et al. (2015) stated that the NAA10 gene is composed of 8 exons.


Mapping

Popp et al. (2015) stated that the NAA10 gene maps to chromosome Xq28.


Gene Function

N-terminal protein acetylation is one of the most common protein modifications that appear to play a role in many biologic processes. The most extensively studied acetylated proteins are the 4 histones, which in all eukaryotic cells organize the nucleosome particles and are subject to an enzyme-catalyzed cycle of acetylation and deacetylation which plays a role in chromatin structure, transcriptional activation, and cell cycle transit. Lack of acetylation of histone H4 distinguishes the inactive from the active mammalian X chromosome (Jeppesen and Turner, 1993).

Using the yeast 2-hybrid system to identify proteins that interact with the ODD domain of HIF1A (603348), Jeong et al. (2002) identified mouse Ard1. They established the function of Ard1 as a protein acetyltransferase in mammalian cells by direct binding to HIF1A to regulate its stability. Jeong et al. (2002) also showed that Ard1-mediated acetylation enhances interaction of HIF1A with VHL (608537) and HIF1A ubiquitination, suggesting that the acetylation of HIF1A by ARD1 is critical to proteasomal degradation. They concluded that the role of ARD1 in the acetylation of HIF1A provides a key regulatory mechanism underlying HIF1A stability. By assaying ARD1 variants expressed in HeLa cells, Kim et al. (2006) determined that mouse Ard1(225), but not mouse or human ARD1(235) strongly decreased VEGF (192240) mRNA expression under hypoxic conditions. As described by Jeong et al. (2002), Ard1(225) mediated epsilon-acetylation of a HIF1A lysine residue; however, mouse and human ARD1(235) had weaker effects. Kim et al. (2006) concluded that the different ARD1 isoforms may have different effects on HIF1A stability and acetylation.

Using in vitro translated mouse proteins, Sugiura et al. (2003) showed that Ard1 and Narg1, which they called Nat1, assembled to form a functional acetyltransferase. Narg1 alone showed no activity. Immunoprecipitation and Western blot analysis demonstrated that Narg1 and Ard1 coassembled in mammalian cells. By cotransfection of rat kidney fibroblasts, they showed that Narg1 and Ard1 localized to the cytoplasm in both overlapping and separate compartments. In situ hybridization demonstrated that during mouse brain development, Narg1 and Ard1 were highly expressed in areas of cell division and migration, and their expression appeared to be downregulated as neurons differentiated. Narg1 and Ard1 were expressed in proliferating mouse embryonic carcinoma cells. Treatment of these cells with retinoic acid initiated neuronal differentiation and downregulation of Narg1 and Ard1 as a neuronal marker gene was induced. Sugiura et al. (2003) concluded that NARG1 and ARD1 play a role in the generation and differentiation of neurons.

Asaumi et al. (2005) confirmed interaction of APP with ARD1 in mammalian cells by coimmunoprecipitation studies. Using human ACTH as a substrate, they showed that the ARD1/NATH (NARG1; 608000) complex has strong N-terminal transferase activity. Immunoprecipitation and Western blotting experiments showed that ARD1 and NATH formed a complex in HEK293 cells. Because APP-binding proteins can modulate APP metabolism, they tested the ability of ARD1 to modulate beta-amyloid-40 secretion and found that coexpression of both ARD1 and NATH was required to suppress beta-amyloid-40 generation from APP. APP endocytosis assay in HEK293 cells showed that ARD1 and NATH suppressed endocytosis of APP.

Using reciprocal immunoprecipitation, followed by mass spectroscopic analysis, Arnesen et al. (2005) showed that endogenous ARD1 and NATH formed stable complexes in several human cell lines and that the complex showed N-terminal acetylation activity. Mutation analysis and examination of proteolytic fragments indicated that interaction was mediated through an N-terminal domain of ARD1 and the C-terminal end of NATH. Immunoprecipitation analysis showed ARD1 and NATH associated with several ribosomal proteins. ARD1 and NATH were also detected in isolated polysomes; however, they were predominantly nonpolysomal. Endogenous ARD1 was present in both the nuclei and cytoplasm in several human cell lines, whereas NATH was predominantly in the cytoplasm, despite the presence of a well-defined nuclear localization signal within the NATH coiled-coil region. Both ARD1 and NATH were cleaved in a caspase-dependent manner during apoptosis in stressed HeLa cells, which resulted in reduced acetylation activity.

Bilton et al. (2005) found no functional relationship between mouse or human ARD1 and HIF1-alpha.


Biochemical Features

Using size-exclusion chromatography, circular dichroism, and fluorescence spectroscopy, Sanchez-Puig and Fersht (2006) found that ARD1 consists of a compact globular region comprising two-thirds of the protein and a flexible unstructured C terminus. In addition, ARD1 could assume a misfolded conformation and form amyloid protofilaments under physiologic conditions of pH and temperature. The process was accelerated by thermal denaturation and high protein concentration. Limited proteolysis of ARD1 protofilaments revealed a proteolysis-resistant core within the acetyltransferase domain.


Molecular Genetics

Ogden Syndrome

Rope et al. (2011) identified a missense mutation in the NAA10 gene (ser37 to pro; 300013.0001) in 2 families segregating a lethal X-linked recessive disorder of infancy, designated Ogden syndrome (OGDNS; 300855), characterized by an aged appearance due to lack of subcutaneous fat and loose skin, and craniofacial anomalies including prominent eyes, large ears, downslanting palpebral fissures, flared nares, hypoplastic alae, short columella, protruding upper lip, and microretrognathia. The boys had initial hypotonia progressing to hypertonia, global developmental delay, usually unilateral cryptorchidism, and cardiac arrhythmias leading to death in the first or second year of life.

In 2 living unrelated children, a boy and a girl, with severe developmental delay and additional features reminiscent of Ogden syndrome, Popp et al. (2015) identified 2 different de novo missense mutations in the NAA10 gene: a hemizygous A116W substitution (300013.0003) in the boy, and a heterozygous V107F substitution (300013.0004) in the girl. The mutations were identified by exome sequencing and confirmed by Sanger sequencing. In vitro functional expression studies showed that the A116W protein had a small but significant reduction in catalytic activity (15% reduction compared to wildtype), whereas the V107F mutant had almost no catalytic activity (about 5% residual activity). Popp et al. (2015) noted that the residual NAA10 activity in their male Swiss patient was significantly higher than that reported by Rope et al. (2011) in the male patients with the S37P mutation (30-70% reduction), which correlated with the less severe phenotype in the Swiss boy.

In 2 young adult brothers, born of unrelated Irish parents, with a variant of Ogden syndrome, Casey et al. (2015) identified a hemizygous missense mutation in the NAA10 gene (Y43S; 300013.0005). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was inherited from the mildly affected mother. In vitro functional expression studies showed that the mutant protein had reduced stability and an 85% reduction in catalytic activity. Casey et al. (2015) noted although that the Y43S mutation resulted in a more severe impairment in catalytic activity compared to the S37P mutation, the Irish brothers had a less severe phenotype than those reported by Rope et al. (2011), indicating that in vitro NAA10 activity in itself may not be sufficient to explain the resulting phenotype.

In 11 unrelated females and a male and female sib pair with Ogden syndrome, Saunier et al. (2016) identified heterozygous mutations and a hemizygous mutation in the NAA10 gene, including 2 novel mutations (R83C, 300013.0010; F128L, 300013.0011) and 3 previously reported mutations (V107F, 300013.0004; R116W, 300013.0003; F128I). The mutations in the 11 unrelated females were de novo and the mutation in the sib pair was due to maternal germline mosaicism. The mutations were identified by whole-exome sequencing or by sequencing of a panel of genes associated with intellectual disability. The R83C mutation was identified in 7 patients, including the sib pair. In vitro enzymatic assays of mutant NAA10 demonstrated reduced catalytic activity with the F108L, V107F, and R83C mutations.

In 22 patients, including 2 males and 20 females, with Ogden syndrome, Cheng et al. (2019) identified hemizygous or heterozygous missense variants in the NAA10 gene, including the recurrent R83C mutation (300013.0010), which occurred de novo in 11 unrelated females. The mutations were found by exome sequencing; none were present in the gnomAD database. In vitro functional expression studies indicated that some of the mutations adversely affected enzymatic activity or stabilization of the NatA complex.

In an 18-year-old woman with Ogden syndrome, Maini et al. (2021) identified heterozygosity for the recurrent R83C mutation in the NAA10 gene. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was shown to be de novo.

In 2 unrelated females and 5 males from 3 families with OGDNS, McTiernan et al. (2022) identified 3 hemizygous (A6P; R79C, 300013.0012; E157K) and 2 heterozygous (F128L, 300013.0011; Q129P) mutations in the NAA10 gene. The hemizygous mutations were maternally inherited and the heterozygous mutations were de novo. In vitro studies in HeLa cells transfected with NAA10 with each mutation demonstrated reduced stability of the A6P, Q129P, and E157K mutants. Coimmunoprecipitation studies of NAA10 with the A6P mutation with NAA15 demonstrated reduced capacity to form the NatA complex. NAA10 with the A6P, R79C, Q129P, and E157K mutations had reduced catalytic activity.

Syndromic Microphthalmia 1

By exome sequencing in 3 affected brothers with Lenz microphthalmia syndrome (MCOPS1; 309800), Esmailpour et al. (2014) identified a splice site mutation in the NAA10 gene (300013.0002) that was confirmed by Sanger sequencing in the 3 sibs and their obligate heterozygote mother, as well as in a maternal aunt and her daughter, but was not found in 4 unaffected family members. There was evidence for reduced expressivity in heterozygotes.

In affected individuals from 3 unrelated families with male-limited syndromic microphthalmia/anophthalmia, Johnston et al. (2019) identified 3 different variants in the 3-prime UTR of the NAA10 gene (300013.0006-300013.0008), all of which altered the consensus polyadenylation sequence. Analysis of X inactivation showed greater than 90% skewing in 4 of 11 carrier females; however, carrier females did not show consistent skewing of X inactivation.


ALLELIC VARIANTS ( 12 Selected Examples):

.0001 OGDEN SYNDROME

NAA10, SER37PRO
  
RCV000022818...

Rope et al. (2011) identified 2 unrelated families segregating a lethal X-linked disorder, Ogden syndrome (OGDNS; 300855). The 2 families had independent occurrences of a T-to-C transition at nucleotide 109 of the NAA10 gene, resulting in a serine-to-proline substitution at codon 37 (S37P). The NAA10 gene encodes the catalytic subunit of the N-terminal acetyltransferase. Substitution of proline for serine at position 37 is likely to affect structure, and in vitro assays of protein function demonstrated 60 to 80% reduction in NAT activity of the mutant protein toward the in vivo substrate RNase P protein p30 (606115). In contrast, the activity toward the substrate high mobility group protein A1 (600701) was reduced by only 20%.

Using structural modeling and simulations, Myklebust et al. (2015) found that S37P mutant NAA10 differs from wildtype NAA10 in regions involved in catalysis and at the interface between NAA10 and NAA15. The S37P mutation shortens helix alpha-2, weakens the interfacial hydrogen-bonding network, and reduces NAA10 flexibility. In vitro biochemical analysis demonstrated reduced substrate binding and catalytic capacity and impaired interaction between S37P mutant NAA10 and NAA15 (608000) or NAA50 (610834). Analysis of total protein N-acetylation in immortalized wildtype and Ogden syndrome B cells and fibroblasts revealed decreased acetylation of a subset of NatA and NatE substrates in Ogden syndrome cells. Furthermore, Ogden syndrome fibroblasts showed reduced cell migration and proliferation capacity, and elevated sensitivity to cell stresses.


.0002 MICROPHTHALMIA, SYNDROMIC 1

NAA10, IVS7DS, T-A, +2
  
RCV000088650

In 3 affected brothers with Lenz microphthalmia syndrome (MCOPS1; 309800), originally studied by Forrester et al. (2001), Esmailpour et al. (2014) identified a c.471+2T-A transversion in intron 7 of the NAA10 gene, predicted to severely alter exon 7 splicing. The mutation was also detected in their obligate heterozygote mother, as well as in a maternal aunt and her daughter, but was not found in 4 unaffected family members. Heterozygous individuals displayed cutaneous syndactyly and short terminal phalanges, features that were not seen in family members who did not carry the mutation. Analysis of patient cDNA revealed the presence of aberrant transcripts. Patient fibroblasts lacked expression of full-length NAA10, and staining suggested that mutant NAA10 aggregated in the cytoplasm; in addition, the fibroblasts displayed cell proliferation defects. Expression studies showed significant dysregulation of microphthalmia-associated genes and their downstream pathways, including STRA6 (610745). Retinol uptake assay showed a significant decrease in retinol uptake by patient fibroblasts compared to controls.


.0003 OGDEN SYNDROME

NAA10, ARG116TRP
   RCV000128609...

In a Swiss boy with a variant of Ogden syndrome (OGDNS; 300855), Popp et al. (2015) identified a de novo hemizygous c.346C-T transition (c.346C-T, NM_003491.3) in the NAA10 gene, resulting in an arg116-to-trp (R116W) substitution at a highly conserved residue in the N-acetyltransferase domain. The mutation, which was found by parent-child trio exome sequencing and confirmed by Sanger sequencing, was not found in the dbSNP (build 137), 1000 Genomes Project, or Exome Sequencing Project databases or in an in-house control database. In vitro functional expression studies showed that the mutant protein had a small but significant reduction in catalytic activity (15% reduction compared to wildtype). The patient had previously been reported in a large exome sequencing study of patients with nonspecific severe intellectual disability (Rauch et al., 2012).

By trio exome sequencing in a female with OGDNS, Saunier et al. (2016) identified de novo heterozygosity for the R116W mutation in the NAA10 gene.


.0004 OGDEN SYNDROME

NAA10, VAL107PHE
  
RCV000128608

In a German girl with a variant of Ogden syndrome (OGDNS; 300855), Popp et al. (2015) identified a de novo heterozygous c.319G-T transversion (c.319G-T, NM_003491.3) in the NAA10 gene, resulting in a val107-to-phe (V107F) substitution at a highly conserved residue in the N-acetyltransferase domain. The mutation, which was found by parent-child trio exome sequencing and confirmed by Sanger sequencing, was not found in the dbSNP (build 137), 1000 Genomes Project, or Exome Sequencing Project databases or in an in-house control database. In vitro functional expression assays showed that the V107F mutant had almost no catalytic activity (about 5% residual activity).

By trio exome sequencing in a female with OGDNS, Saunier et al. (2016) identified de novo heterozygosity for the V107F mutation in the NAA10 gene.


.0005 OGDEN SYNDROME

NAA10, TYR43SER
  
RCV000202352

In 2 young adult brothers, born of unrelated Irish parents, with a variant of Ogden syndrome (OGDNS; 300855), Casey et al. (2015) identified a hemizygous c.128A-C transversion (c.128A-C, NM_001256120.1) in the NAA10 gene, resulting in a tyr43-to-ser (Y43S) substitution at a highly conserved residue. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not found in the dbSNP, 1000 Genomes Project, or Exome Variant Server databases and was demonstrated to be inherited from the mildly affected mother. In vitro functional expression studies showed that the mutant protein had reduced stability and an 85% reduction in catalytic activity.


.0006 MICROPHTHALMIA, SYNDROMIC 1

NAA10, +43A-G, 3-PRIME UTR
  
RCV001215735

In a 3-generation family from Northern Ireland (family 1) with syndromic microphthalmia (MCOPS1; 309800), originally reported by Graham et al. (1988, 1991), Johnston et al. (2019) identified a c.*43A-G transition (c.*43A-G, NM_003491.3) in the 3-prime UTR of the NAA10 gene (chrX:153,195,397T-C, GRCh37), altering the consensus polyadenylation sequence (PAS) from AATAAA to AATAGA. The mutation, which was not found in the gnomAD database, segregated fully with disease in the family, including in 1 male previously thought to be unaffected, but who exhibited cleft soft palate and an ear tag. One carrier female showed greater than 90% skewing of X inactivation, but the authors noted that females did not show consistent skewing of X inactivation. Analysis by qPCR of patient mRNA showed an approximately 50% decrease in NAA10 mRNA compared to controls, whereas carrier females had similar levels to controls. RNAseq analysis of transcript structure in affected individuals revealed that read depth did not decrease as expected at the PAS in the 3-prime UTR, but declined approximately 600 bp further 3-prime at a predicted second PAS.


.0007 MICROPHTHALMIA, SYNDROMIC 1

NAA10, +39A-G, 3-PRIME UTR
  
RCV001215737...

In a 5-generation family (family 2) with syndromic microphthalmia (MCOPS1; 309800), originally reported by Slavotinek et al. (2005), Johnston et al. (2019) identified a c.*39A-G transition (c.*39A-G, NM_003491.3) in the 3-prime UTR of the NAA10 gene (chrX:153,195,401T-C, GRCh37), altering the consensus polyadenylation sequence (PAS) from AATAAA to GATAAA. The mutation segregated with disease in the family. Three carrier females showed greater than 90% skewing of X inactivation, but the authors noted that females did not show consistent skewing of X inactivation. Analysis by qPCR of patient mRNA showed an approximately 50% decrease in NAA10 mRNA compared to controls, whereas carrier females had similar levels to controls. RNAseq analysis of transcript structure in affected individuals revealed that read depth did not decrease as expected at the PAS in the 3-prime UTR, but declined approximately 600 bp further 3-prime at a predicted second PAS.


.0008 MICROPHTHALMIA, SYNDROMIC 1

NAA10, +40A-G, 3-PRIME UTR
  
RCV001215739...

In an 8-month-old boy (family 3) with syndromic microphthalmia (MCOPS1; 309800), Johnston et al. (2019) identified a c.*40A-G transition (c.*40A-G, NM_003491.3) in the 3-prime UTR of the NAA10 gene (chrX:153,195,400T-C, GRCh37), altering the consensus polyadenylation sequence (PAS) from AATAAA to AGTAAA. The mutation was present in his unaffected carrier mother.


.0009 MICROPHTHALMIA, SYNDROMIC 1

NAA10, 4-BP DEL
  
RCV001375494...

In an 11-year-old boy (patient 23) with syndromic microphthalmia-1 (MCOPS1; 309800), Cheng et al. (2019) identified a 4-bp deletion (c.455_458del) in the NAA10 gene, resulting in a frameshift and premature termination (Thr152ArgfsTer6). The mutation was inherited from his mother.


.0010 OGDEN SYNDROME

NAA10, ARG83CYS
   RCV000190675...

In 6 unrelated females and a brother-sister pair with Ogden syndrome (OGDNS; 300855), Saunier et al. (2016) identified heterozygosity or hemizygosity for a c.247C-T transition (c.247C-T, NM_003491.3) in the NAA10 gene, resulting in an arg83-to-cys (R83C) substitution. The mutations, which were found by trio whole-exome sequencing or by sequencing of a panel of genes associated with intellectual disability, were de novo in the 11 unrelated females and were due to maternal germline mosaicism in the sib pair. In vitro assays of mutant NAA10 with the R83C mutation demonstrated reduced catalytic activity and a higher Km compared to wildtype, indicating reduced affinity to acetyl-CoA.

In 11 unrelated females with OGDNS, Cheng et al. (2019) identified a de novo heterozygous c.247C-T transition in exon 5 of the NAA10 gene, resulting in an R83C substitution. The mutation was found by exome sequencing; it was not present in the gnomAD database. In vitro functional expression studies indicated that the mutation may have increased activity compared to wildtype in certain circumstances.

In an 18-year-old woman with OGDNS, Maini et al. (2021) identified heterozygosity for the R83C mutation in the NAA10 gene. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was shown to be de novo.


.0011 OGDEN SYNDROME

NAA10, PHE128LEU
   RCV000225366...

In 2 unrelated female patients (patients 3 and 4) with Ogden syndrome (OGDNS; 300855), Saunier et al. (2016) identified a de novo heterozygous c.384T-A transversion (c.384T-A, NM_003491.3) in the NAA10 gene, resulting in a phe128-to-leu (F128L) substitution. The mutation was found by trio whole-exome sequencing and confirmed by Sanger sequencing. In vitro assays of mutant NAA10 with the F128L mutation demonstrated reduced protein stability.


.0012 OGDEN SYNDROME

NAA10, ARG79CYS
  
RCV000436076...

In 2 brothers (individuals 4 and 5) and a maternal uncle (individual 3) with Ogden syndrome (OGDNS; 300855), McTiernan et al. (2022) identified a c.235C-T transition (c.235C-T, NM_003491.4) in the NAA10 gene, resulting in an arg79-to-cys (R79C) substitution. The mutation was identified by whole-exome sequencing. Another maternal uncle (individual 2) was similarly affected but did not undergo molecular testing. In vitro studies of NAA10 with the R79C mutation had reduced Nt-acetylation catalytic activity towards a synthetic oligopeptide compared to wildtype NAA10.


REFERENCES

  1. Arnesen, T., Anderson, D., Baldersheim, C., Lanotte, M., Varhaug, J. E., Lillehaug, J. R. Identification and characterization of the human ARD1-NATH protein acetyltransferase complex. Biochem. J. 386: 433-443, 2005. [PubMed: 15496142, images, related citations] [Full Text]

  2. Asaumi, M., Iijima, K., Sumioka, A., Iijima-Ando, K., Kirino, Y., Nakaya, T., Suzuki, T. Interaction of N-terminal acetyltransferase with the cytoplasmic domain of beta-amyloid precursor protein and its effect on A-beta secretion. J. Biochem. 137: 147-155, 2005. [PubMed: 15749829, related citations] [Full Text]

  3. Bilton, R., Mazure, N., Trottier, E., Hattab, M., Dery, M.-A., Richard, D. E., Pouyssegur, J., Brahimi-Horn, M. C. Arrest-defective-1 protein, an acetyltransferase, does not alter stability of hypoxia-inducible factor (HIF)-1-alpha and is not induced by hypoxia or HIF. J. Biol. Chem. 280: 31132-31140, 2005. Note: Erratum: J. Biol. Chem. 281: 15592 only, 2006. [PubMed: 15994306, related citations] [Full Text]

  4. Casey, J. P., Stove, S. I., McGorrian, C., Galvin, J., Blenski, M., Dunne, A., Ennis, S., Brett, F., King, M. D., Arnesen, T., Lynch, S. A. NAA10 mutation causing a novel intellectual disability syndrome with long QT due to N-terminal acetyltransferase impairment. Sci. Rep. 5: 16022, 2015. Note: Electronic Article. [PubMed: 26522270, images, related citations] [Full Text]

  5. Cheng, H., Gottlieb, L., Marchi, E., Kleyner, R., Bhardwaj, P., Rope, A. F., Rosenheck, S., Moutton, S., Philippe, C., Eyaid, W., Alkuraya, F. S., Toribio, J., and 17 others. Phenotypic and biochemical analysis of an international cohort of individuals with variants in NAA10 and NAA15. Hum. Molec. Genet. 28: 2900-2919, 2019. Note: Erratum: Hum. Molec. Genet. 29: 877-878, 2020. [PubMed: 31127942, images, related citations] [Full Text]

  6. Esmailpour, T., Riazifar, H., Liu, L., Donkervoort, S., Huang, V. H., Madaan, S., Shoucri, B. M., Busch, A., Wu, J., Towbin, A., Chadwick, R. B., Sequeira, A., Vawter, M. P., Sun, G., Johnston, J. J., Biesecker, L. G., Kawaguchi, R., Sun, H., Kimonis, V., Huang, T. A splice donor mutation in NAA10 results in the dysregulation of the retinoic acid signalling pathway and causes Lenz microphthalmia syndrome. J. Med. Genet. 51: 185-196, 2014. [PubMed: 24431331, images, related citations] [Full Text]

  7. Forrester, S., Kovach, M. J., Reynolds, N. M., Urban, R., Kimonis, V. Manifestations in four males with and an obligate carrier of the Lenz microphthalmia syndrome. Am. J. Med. Genet. 98: 92-100, 2001. [PubMed: 11426460, related citations]

  8. Graham, C. A., McCleary, B. G., Malcolm, S., Kelly, E. D., Hill, A. J., Johnston, W. P., Nevin, N. C. Linkage analysis in a family with X-linked anophthalmos. (Abstract) J. Med. Genet. 25: 643 only, 1988.

  9. Graham, C. A., Redmond, R. M., Nevin, N. C. X-linked clinical anophthalmos: localization of the gene to Xq27-Xq28. Ophthalmic Paediat. Genet. 12: 43-48, 1991. [PubMed: 1679229, related citations] [Full Text]

  10. Jeong, J.-W., Bae, M.-K., Ahn, M.-Y., Kim, S.-H., Sohn, T.-K., Bae, M.-H., Yoo, M.-A., Song, E. J., Lee, K.-J., Kim, K.-W. Regulation and destabilization of HIF-1-alpha by ARD1-mediated acetylation. Cell 111: 709-720, 2002. [PubMed: 12464182, related citations] [Full Text]

  11. Jeppesen, P., Turner, B. M. The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74: 281-289, 1993. [PubMed: 8343956, related citations] [Full Text]

  12. Johnston, J. J., Williamson, K. A., Chou, C. M., Sapp, J. C., Ansari, M., Chapman, H. M., Cooper, D. N., Dabib, T., Dudley, J. N., Holt, R. J., Ragge, N. K., Schaffer, A. A., Sen, S. K., Slavotinek, A. M., FitzPatrick, D. R., Glaser, T. M., Stewart, F., Black, G. C. M., Biesecker, L. G. NAA10 polyadenylation signal variants cause syndromic microphthalmia. J. Med. Genet. 56: 444-453, 2019. [PubMed: 30842225, images, related citations] [Full Text]

  13. Kim, S.-H., Park, J. A., Kim, J. H., Lee, J.-W., Seo, J. H., Jung, B.-K., Chun, K.-H., Jeong, J.-W., Bae, M.-K., Kim, K.-W. Characterization of ARD1 variants in mammalian cells. Biochem. Biophys. Res. Commun. 340: 422-427, 2006. [PubMed: 16376303, related citations] [Full Text]

  14. Maini, I., Caraffi, S. G., Peluso, F., Valeri, L., Nicoli, D., Laurie, S., Baldo, C., Zuffardi, O., Garavelli, L. Clinical Manifestations in a girl with NAA10-related syndrome and genotype-phenotype correlation in females. Genes (Basel) 12: 900, 2021. [PubMed: 34200686, images, related citations] [Full Text]

  15. McTiernan, N., Tranebjaerg, L., Bjorheim, A. S., Hogue, J. S., Wilson, W. G., Schmidt, B., Boerrigter, M. M., Nybo, M. L., Smeland, M. F., Tumer, Z., Arnesen, T. Biochemical analysis of novel NAA10 variants suggests distinct pathogenic mechanisms involving impaired protein N-terminal acetylation. Hum. Genet. 141: 1355-1369, 2022. [PubMed: 35039925, images, related citations] [Full Text]

  16. Myklebust, L. M., Van Damme, P., Stove, S. I., Dorfel, M. J., Abboud, A., Kalvik, T. V., Grauffel, C., Jonckheere, V., Wu, Y., Swensen, J., Kaasa, H., Liszczak, G., Marmorstein, R., Reuter, N., Lyon, G. J., Gevaert, K., Arnesen, T. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Hum. Molec. Genet. 24: 1956-1976, 2015. [PubMed: 25489052, images, related citations] [Full Text]

  17. Popp, B., Stove, S. I., Endele, S., Myklebust, L. M., Hoyer, J., Sticht, H., Azzarello-Burri, S., Rauch, A., Arnesen, T., Reis, A. De novo missense mutations in the NAA10 gene cause severe non-syndromic developmental delay in males and females. Europ. J. Hum. Genet. 23: 602-609, 2015. [PubMed: 25099252, images, related citations] [Full Text]

  18. Rauch, A., Wieczorek, D., Graf, E., Wieland, T., Endele, S., Schwarzmayr, T., Albrecht, B., Bartholdi, D., Beygo, J., Di Donato, N., Dufke, A., Cremer, K., and 27 others. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380: 1674-1682, 2012. [PubMed: 23020937, related citations] [Full Text]

  19. Rope, A. F., Wang, K., Evjenth, R., Xing, J., Johnston, J. J., Swensen, J. J., Johnson, W. E., Moore, B., Huff, C. D., Bird, L. M., Carey, J. C., Opitz, J. M., and 16 others. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am. J. Hum. Genet. 89: 28-43, 2011. Note: Erratum: Am. J. Hum. Genet. 89: 345 only, 2011. [PubMed: 21700266, images, related citations] [Full Text]

  20. Sanchez-Puig, N., Fersht, A. R. Characterization of the native and fibrillar conformation of the human N-alpha-acetyltransferase ARD1. Protein Sci. 15: 1968-1976, 2006. [PubMed: 16823041, images, related citations] [Full Text]

  21. Saunier, C., Stove, S. I., Popp, B., Gerard, B., Blenski, M., AhMew, N., de Bie, C., Goldenberg, P., Isidor, B., Keren, B., Leheup, B., Lampert, L., and 19 others. Expanding the phenotype associated with NAA10-related N-terminal acetylation deficiency. Hum. Mutat. 37: 755-64, 2016. [PubMed: 27094817, images, related citations] [Full Text]

  22. Slavotinek, A., Lee, S. S., Hamilton, S. P. A family with X-linked anophthalmia: exclusion of SOX3 as a candidate gene. Am. J. Med. Genet. 138A: 89-94, 2005. [PubMed: 16114045, related citations] [Full Text]

  23. Sugiura, N., Adams, S. M., Corriveau, R. A. An evolutionarily conserved N-terminal acetyltransferase complex associated with neuronal development. J. Biol. Chem. 278: 40113-40120, 2003. [PubMed: 12888564, related citations] [Full Text]

  24. Tribioli, C., Mancini, M., Plassart, E., Bione, S., Rivella, S., Sala, C., Torri, G., Toniolo, D. Isolation of new genes in distal Xq28: transcriptional map and identification of a human homologue of the ARD1 N-acetyltransferase of Saccharomyces cerevisiae. Hum. Molec. Genet. 3: 1061-1067, 1994. [PubMed: 7981673, related citations] [Full Text]

  25. Whiteway, M., Szostak, J. W. The ARD1 gene of yeast functions in the switch between the mitotic cell cycle and alternative developmental pathways. Cell 43: 483-492, 1985. [PubMed: 3907857, related citations] [Full Text]


Hilary J. Vernon - updated : 09/08/2022
Cassandra L. Kniffin - updated : 06/17/2021
Carol A. Bocchini - updated : 04/26/2021
Marla J. F. O'Neill - updated : 07/10/2020
Marla J. F. O'Neill - updated : 07/10/2020
Patricia A. Hartz - updated : 10/28/2016
Cassandra L. Kniffin - updated : 11/23/2015
Marla J. F. O'Neill - updated : 1/29/2014
Ada Hamosh - updated : 8/19/2011
Patricia A. Hartz - updated : 3/6/2007
Stefanie A. Nelson - updated : 2/22/2007
Stylianos E. Antonarakis - updated : 1/17/2003
Creation Date:
Victor A. McKusick : 2/4/1996
carol : 09/09/2022
carol : 09/08/2022
carol : 11/10/2021
alopez : 07/07/2021
ckniffin : 06/17/2021
carol : 05/05/2021
carol : 04/26/2021
alopez : 07/10/2020
alopez : 07/10/2020
carol : 10/20/2017
carol : 08/24/2017
alopez : 06/28/2017
alopez : 10/28/2016
carol : 11/24/2015
ckniffin : 11/23/2015
mcolton : 8/7/2014
carol : 1/29/2014
mcolton : 1/28/2014
carol : 12/20/2011
carol : 9/13/2011
alopez : 9/12/2011
alopez : 8/24/2011
alopez : 8/24/2011
terry : 8/19/2011
carol : 7/6/2011
alopez : 6/17/2010
wwang : 3/6/2007
wwang : 2/22/2007
ckniffin : 8/3/2005
ckniffin : 3/23/2004
mgross : 1/17/2003
mgross : 1/17/2003
joanna : 8/31/1998
joanna : 8/31/1998
joanna : 2/4/1996
joanna : 2/4/1996

* 300013

N-ALPHA-ACETYLTRANSFERASE 10, NatA CATALYTIC SUBUNIT; NAA10


Alternative titles; symbols

ARD1 N-ACETYLTRANSFERASE, S. CEREVISIAE, HOMOLOG OF, A; ARD1A
ARREST-DEFECTIVE PROTEIN 1; ARD1
TE2


HGNC Approved Gene Symbol: NAA10

SNOMEDCT: 438504004, 771442003;  


Cytogenetic location: Xq28   Genomic coordinates (GRCh38) : X:153,929,225-153,935,037 (from NCBI)


Gene-Phenotype Relationships

Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
Xq28 Microphthalmia, syndromic 1 309800 X-linked 3
Ogden syndrome 300855 X-linked dominant; X-linked recessive 3

TEXT

Description

N-alpha-acetylation is a common protein modification that occurs during protein synthesis and involves the transfer of an acetyl group from acetyl-coenzyme A to the protein alpha-amino group. ARD1A, together with NATH (NARG1, NAA15; 608000), is part of a major N-alpha-acetyltransferase complex responsible for alpha-acetylation of proteins and peptides (Sanchez-Puig and Fersht, 2006).


Cloning and Expression

Tribioli et al. (1994) described the physical and transcriptional organization of a region of 140 kb in Xq28, 5-prime to the L1CAM gene (308840). They established a transcriptional map of the region by isolating and mapping CpG islands to the physical map, determining partial nucleotide sequences, and studying the pattern of expression and orientation of the transcripts. They succeeded in positioning 4 previously identified genes: L1CAM, AVPR2 (300538), HFC1 (300019), and RENBP (312420). All genes in the region are rather small, ranging in size from 2 to 30 kb, and very close to one another. With the exception of the AVPR2 gene, they serve a housekeeping function, having a CpG island at their 5-prime end and the same orientation of transcription. This kind of organization is consistent with the one previously described for the more distal portion of Xq28, between the color vision pigment genes and the G6PD gene and indicates that genes with a housekeeping and tissue-specific pattern of expression are interspersed in the genome but are probably found in different 'transcriptional domains' (characterized by different orientation). Three new genes were identified and positioned. One of these, termed TE2, demonstrated 40% identity with the ARD1 protein of Saccharomyces cerevisiae (Whiteway and Szostak, 1985), a protein required for the expression of an N-terminal protein acetyltransferase activity.

Using Northern blot analysis, Sugiura et al. (2003) showed mouse Ard1 was ubiquitously expressed. By database analysis and PCR, Kim et al. (2006) identified 3 splice variants of mouse Ard1 and 2 splice variants of human ARD1. The mouse variants encoded proteins of 235-, 225-, and 198-amino acids. Ard1(235) and Ard1(225) have well-conserved N-acetyltransferase domains, but Ard1(198) has only a partial domain. The human ARD1 variants encoded proteins of 131- and 235-amino acids. The C-terminal region of mouse Ard1(225) differs from that of both mouse and human ARD1(235), likely due to alternative splicing of exon 8. Western blot analysis of human cell lines showed a major intense band of about 32 kD, which corresponded to ARD1(235). In contrast, mouse fibroblasts strongly expressed a 30-kD protein, corresponding to Ard1(225).

Asaumi et al. (2005) cloned ARD1 and identified it as a potential APP (104760)-binding protein in a yeast 2-hybrid assay. The 235-amino acid protein contains an N-acetyltransferase domain, a highly conserved acetyl-coenzyme A binding motif, and a C-terminal APP-binding domain.


Gene Structure

Popp et al. (2015) stated that the NAA10 gene is composed of 8 exons.


Mapping

Popp et al. (2015) stated that the NAA10 gene maps to chromosome Xq28.


Gene Function

N-terminal protein acetylation is one of the most common protein modifications that appear to play a role in many biologic processes. The most extensively studied acetylated proteins are the 4 histones, which in all eukaryotic cells organize the nucleosome particles and are subject to an enzyme-catalyzed cycle of acetylation and deacetylation which plays a role in chromatin structure, transcriptional activation, and cell cycle transit. Lack of acetylation of histone H4 distinguishes the inactive from the active mammalian X chromosome (Jeppesen and Turner, 1993).

Using the yeast 2-hybrid system to identify proteins that interact with the ODD domain of HIF1A (603348), Jeong et al. (2002) identified mouse Ard1. They established the function of Ard1 as a protein acetyltransferase in mammalian cells by direct binding to HIF1A to regulate its stability. Jeong et al. (2002) also showed that Ard1-mediated acetylation enhances interaction of HIF1A with VHL (608537) and HIF1A ubiquitination, suggesting that the acetylation of HIF1A by ARD1 is critical to proteasomal degradation. They concluded that the role of ARD1 in the acetylation of HIF1A provides a key regulatory mechanism underlying HIF1A stability. By assaying ARD1 variants expressed in HeLa cells, Kim et al. (2006) determined that mouse Ard1(225), but not mouse or human ARD1(235) strongly decreased VEGF (192240) mRNA expression under hypoxic conditions. As described by Jeong et al. (2002), Ard1(225) mediated epsilon-acetylation of a HIF1A lysine residue; however, mouse and human ARD1(235) had weaker effects. Kim et al. (2006) concluded that the different ARD1 isoforms may have different effects on HIF1A stability and acetylation.

Using in vitro translated mouse proteins, Sugiura et al. (2003) showed that Ard1 and Narg1, which they called Nat1, assembled to form a functional acetyltransferase. Narg1 alone showed no activity. Immunoprecipitation and Western blot analysis demonstrated that Narg1 and Ard1 coassembled in mammalian cells. By cotransfection of rat kidney fibroblasts, they showed that Narg1 and Ard1 localized to the cytoplasm in both overlapping and separate compartments. In situ hybridization demonstrated that during mouse brain development, Narg1 and Ard1 were highly expressed in areas of cell division and migration, and their expression appeared to be downregulated as neurons differentiated. Narg1 and Ard1 were expressed in proliferating mouse embryonic carcinoma cells. Treatment of these cells with retinoic acid initiated neuronal differentiation and downregulation of Narg1 and Ard1 as a neuronal marker gene was induced. Sugiura et al. (2003) concluded that NARG1 and ARD1 play a role in the generation and differentiation of neurons.

Asaumi et al. (2005) confirmed interaction of APP with ARD1 in mammalian cells by coimmunoprecipitation studies. Using human ACTH as a substrate, they showed that the ARD1/NATH (NARG1; 608000) complex has strong N-terminal transferase activity. Immunoprecipitation and Western blotting experiments showed that ARD1 and NATH formed a complex in HEK293 cells. Because APP-binding proteins can modulate APP metabolism, they tested the ability of ARD1 to modulate beta-amyloid-40 secretion and found that coexpression of both ARD1 and NATH was required to suppress beta-amyloid-40 generation from APP. APP endocytosis assay in HEK293 cells showed that ARD1 and NATH suppressed endocytosis of APP.

Using reciprocal immunoprecipitation, followed by mass spectroscopic analysis, Arnesen et al. (2005) showed that endogenous ARD1 and NATH formed stable complexes in several human cell lines and that the complex showed N-terminal acetylation activity. Mutation analysis and examination of proteolytic fragments indicated that interaction was mediated through an N-terminal domain of ARD1 and the C-terminal end of NATH. Immunoprecipitation analysis showed ARD1 and NATH associated with several ribosomal proteins. ARD1 and NATH were also detected in isolated polysomes; however, they were predominantly nonpolysomal. Endogenous ARD1 was present in both the nuclei and cytoplasm in several human cell lines, whereas NATH was predominantly in the cytoplasm, despite the presence of a well-defined nuclear localization signal within the NATH coiled-coil region. Both ARD1 and NATH were cleaved in a caspase-dependent manner during apoptosis in stressed HeLa cells, which resulted in reduced acetylation activity.

Bilton et al. (2005) found no functional relationship between mouse or human ARD1 and HIF1-alpha.


Biochemical Features

Using size-exclusion chromatography, circular dichroism, and fluorescence spectroscopy, Sanchez-Puig and Fersht (2006) found that ARD1 consists of a compact globular region comprising two-thirds of the protein and a flexible unstructured C terminus. In addition, ARD1 could assume a misfolded conformation and form amyloid protofilaments under physiologic conditions of pH and temperature. The process was accelerated by thermal denaturation and high protein concentration. Limited proteolysis of ARD1 protofilaments revealed a proteolysis-resistant core within the acetyltransferase domain.


Molecular Genetics

Ogden Syndrome

Rope et al. (2011) identified a missense mutation in the NAA10 gene (ser37 to pro; 300013.0001) in 2 families segregating a lethal X-linked recessive disorder of infancy, designated Ogden syndrome (OGDNS; 300855), characterized by an aged appearance due to lack of subcutaneous fat and loose skin, and craniofacial anomalies including prominent eyes, large ears, downslanting palpebral fissures, flared nares, hypoplastic alae, short columella, protruding upper lip, and microretrognathia. The boys had initial hypotonia progressing to hypertonia, global developmental delay, usually unilateral cryptorchidism, and cardiac arrhythmias leading to death in the first or second year of life.

In 2 living unrelated children, a boy and a girl, with severe developmental delay and additional features reminiscent of Ogden syndrome, Popp et al. (2015) identified 2 different de novo missense mutations in the NAA10 gene: a hemizygous A116W substitution (300013.0003) in the boy, and a heterozygous V107F substitution (300013.0004) in the girl. The mutations were identified by exome sequencing and confirmed by Sanger sequencing. In vitro functional expression studies showed that the A116W protein had a small but significant reduction in catalytic activity (15% reduction compared to wildtype), whereas the V107F mutant had almost no catalytic activity (about 5% residual activity). Popp et al. (2015) noted that the residual NAA10 activity in their male Swiss patient was significantly higher than that reported by Rope et al. (2011) in the male patients with the S37P mutation (30-70% reduction), which correlated with the less severe phenotype in the Swiss boy.

In 2 young adult brothers, born of unrelated Irish parents, with a variant of Ogden syndrome, Casey et al. (2015) identified a hemizygous missense mutation in the NAA10 gene (Y43S; 300013.0005). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was inherited from the mildly affected mother. In vitro functional expression studies showed that the mutant protein had reduced stability and an 85% reduction in catalytic activity. Casey et al. (2015) noted although that the Y43S mutation resulted in a more severe impairment in catalytic activity compared to the S37P mutation, the Irish brothers had a less severe phenotype than those reported by Rope et al. (2011), indicating that in vitro NAA10 activity in itself may not be sufficient to explain the resulting phenotype.

In 11 unrelated females and a male and female sib pair with Ogden syndrome, Saunier et al. (2016) identified heterozygous mutations and a hemizygous mutation in the NAA10 gene, including 2 novel mutations (R83C, 300013.0010; F128L, 300013.0011) and 3 previously reported mutations (V107F, 300013.0004; R116W, 300013.0003; F128I). The mutations in the 11 unrelated females were de novo and the mutation in the sib pair was due to maternal germline mosaicism. The mutations were identified by whole-exome sequencing or by sequencing of a panel of genes associated with intellectual disability. The R83C mutation was identified in 7 patients, including the sib pair. In vitro enzymatic assays of mutant NAA10 demonstrated reduced catalytic activity with the F108L, V107F, and R83C mutations.

In 22 patients, including 2 males and 20 females, with Ogden syndrome, Cheng et al. (2019) identified hemizygous or heterozygous missense variants in the NAA10 gene, including the recurrent R83C mutation (300013.0010), which occurred de novo in 11 unrelated females. The mutations were found by exome sequencing; none were present in the gnomAD database. In vitro functional expression studies indicated that some of the mutations adversely affected enzymatic activity or stabilization of the NatA complex.

In an 18-year-old woman with Ogden syndrome, Maini et al. (2021) identified heterozygosity for the recurrent R83C mutation in the NAA10 gene. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was shown to be de novo.

In 2 unrelated females and 5 males from 3 families with OGDNS, McTiernan et al. (2022) identified 3 hemizygous (A6P; R79C, 300013.0012; E157K) and 2 heterozygous (F128L, 300013.0011; Q129P) mutations in the NAA10 gene. The hemizygous mutations were maternally inherited and the heterozygous mutations were de novo. In vitro studies in HeLa cells transfected with NAA10 with each mutation demonstrated reduced stability of the A6P, Q129P, and E157K mutants. Coimmunoprecipitation studies of NAA10 with the A6P mutation with NAA15 demonstrated reduced capacity to form the NatA complex. NAA10 with the A6P, R79C, Q129P, and E157K mutations had reduced catalytic activity.

Syndromic Microphthalmia 1

By exome sequencing in 3 affected brothers with Lenz microphthalmia syndrome (MCOPS1; 309800), Esmailpour et al. (2014) identified a splice site mutation in the NAA10 gene (300013.0002) that was confirmed by Sanger sequencing in the 3 sibs and their obligate heterozygote mother, as well as in a maternal aunt and her daughter, but was not found in 4 unaffected family members. There was evidence for reduced expressivity in heterozygotes.

In affected individuals from 3 unrelated families with male-limited syndromic microphthalmia/anophthalmia, Johnston et al. (2019) identified 3 different variants in the 3-prime UTR of the NAA10 gene (300013.0006-300013.0008), all of which altered the consensus polyadenylation sequence. Analysis of X inactivation showed greater than 90% skewing in 4 of 11 carrier females; however, carrier females did not show consistent skewing of X inactivation.


ALLELIC VARIANTS 12 Selected Examples):

.0001   OGDEN SYNDROME

NAA10, SER37PRO
SNP: rs387906701, ClinVar: RCV000022818, RCV005055521

Rope et al. (2011) identified 2 unrelated families segregating a lethal X-linked disorder, Ogden syndrome (OGDNS; 300855). The 2 families had independent occurrences of a T-to-C transition at nucleotide 109 of the NAA10 gene, resulting in a serine-to-proline substitution at codon 37 (S37P). The NAA10 gene encodes the catalytic subunit of the N-terminal acetyltransferase. Substitution of proline for serine at position 37 is likely to affect structure, and in vitro assays of protein function demonstrated 60 to 80% reduction in NAT activity of the mutant protein toward the in vivo substrate RNase P protein p30 (606115). In contrast, the activity toward the substrate high mobility group protein A1 (600701) was reduced by only 20%.

Using structural modeling and simulations, Myklebust et al. (2015) found that S37P mutant NAA10 differs from wildtype NAA10 in regions involved in catalysis and at the interface between NAA10 and NAA15. The S37P mutation shortens helix alpha-2, weakens the interfacial hydrogen-bonding network, and reduces NAA10 flexibility. In vitro biochemical analysis demonstrated reduced substrate binding and catalytic capacity and impaired interaction between S37P mutant NAA10 and NAA15 (608000) or NAA50 (610834). Analysis of total protein N-acetylation in immortalized wildtype and Ogden syndrome B cells and fibroblasts revealed decreased acetylation of a subset of NatA and NatE substrates in Ogden syndrome cells. Furthermore, Ogden syndrome fibroblasts showed reduced cell migration and proliferation capacity, and elevated sensitivity to cell stresses.


.0002   MICROPHTHALMIA, SYNDROMIC 1

NAA10, IVS7DS, T-A, +2
SNP: rs587776457, ClinVar: RCV000088650

In 3 affected brothers with Lenz microphthalmia syndrome (MCOPS1; 309800), originally studied by Forrester et al. (2001), Esmailpour et al. (2014) identified a c.471+2T-A transversion in intron 7 of the NAA10 gene, predicted to severely alter exon 7 splicing. The mutation was also detected in their obligate heterozygote mother, as well as in a maternal aunt and her daughter, but was not found in 4 unaffected family members. Heterozygous individuals displayed cutaneous syndactyly and short terminal phalanges, features that were not seen in family members who did not carry the mutation. Analysis of patient cDNA revealed the presence of aberrant transcripts. Patient fibroblasts lacked expression of full-length NAA10, and staining suggested that mutant NAA10 aggregated in the cytoplasm; in addition, the fibroblasts displayed cell proliferation defects. Expression studies showed significant dysregulation of microphthalmia-associated genes and their downstream pathways, including STRA6 (610745). Retinol uptake assay showed a significant decrease in retinol uptake by patient fibroblasts compared to controls.


.0003   OGDEN SYNDROME

NAA10, ARG116TRP
ClinVar: RCV000128609, RCV000413890, RCV004528848

In a Swiss boy with a variant of Ogden syndrome (OGDNS; 300855), Popp et al. (2015) identified a de novo hemizygous c.346C-T transition (c.346C-T, NM_003491.3) in the NAA10 gene, resulting in an arg116-to-trp (R116W) substitution at a highly conserved residue in the N-acetyltransferase domain. The mutation, which was found by parent-child trio exome sequencing and confirmed by Sanger sequencing, was not found in the dbSNP (build 137), 1000 Genomes Project, or Exome Sequencing Project databases or in an in-house control database. In vitro functional expression studies showed that the mutant protein had a small but significant reduction in catalytic activity (15% reduction compared to wildtype). The patient had previously been reported in a large exome sequencing study of patients with nonspecific severe intellectual disability (Rauch et al., 2012).

By trio exome sequencing in a female with OGDNS, Saunier et al. (2016) identified de novo heterozygosity for the R116W mutation in the NAA10 gene.


.0004   OGDEN SYNDROME

NAA10, VAL107PHE
SNP: rs587780562, ClinVar: RCV000128608

In a German girl with a variant of Ogden syndrome (OGDNS; 300855), Popp et al. (2015) identified a de novo heterozygous c.319G-T transversion (c.319G-T, NM_003491.3) in the NAA10 gene, resulting in a val107-to-phe (V107F) substitution at a highly conserved residue in the N-acetyltransferase domain. The mutation, which was found by parent-child trio exome sequencing and confirmed by Sanger sequencing, was not found in the dbSNP (build 137), 1000 Genomes Project, or Exome Sequencing Project databases or in an in-house control database. In vitro functional expression assays showed that the V107F mutant had almost no catalytic activity (about 5% residual activity).

By trio exome sequencing in a female with OGDNS, Saunier et al. (2016) identified de novo heterozygosity for the V107F mutation in the NAA10 gene.


.0005   OGDEN SYNDROME

NAA10, TYR43SER
SNP: rs863225427, ClinVar: RCV000202352

In 2 young adult brothers, born of unrelated Irish parents, with a variant of Ogden syndrome (OGDNS; 300855), Casey et al. (2015) identified a hemizygous c.128A-C transversion (c.128A-C, NM_001256120.1) in the NAA10 gene, resulting in a tyr43-to-ser (Y43S) substitution at a highly conserved residue. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not found in the dbSNP, 1000 Genomes Project, or Exome Variant Server databases and was demonstrated to be inherited from the mildly affected mother. In vitro functional expression studies showed that the mutant protein had reduced stability and an 85% reduction in catalytic activity.


.0006   MICROPHTHALMIA, SYNDROMIC 1

NAA10, +43A-G, 3-PRIME UTR
SNP: rs1603289772, ClinVar: RCV001215735

In a 3-generation family from Northern Ireland (family 1) with syndromic microphthalmia (MCOPS1; 309800), originally reported by Graham et al. (1988, 1991), Johnston et al. (2019) identified a c.*43A-G transition (c.*43A-G, NM_003491.3) in the 3-prime UTR of the NAA10 gene (chrX:153,195,397T-C, GRCh37), altering the consensus polyadenylation sequence (PAS) from AATAAA to AATAGA. The mutation, which was not found in the gnomAD database, segregated fully with disease in the family, including in 1 male previously thought to be unaffected, but who exhibited cleft soft palate and an ear tag. One carrier female showed greater than 90% skewing of X inactivation, but the authors noted that females did not show consistent skewing of X inactivation. Analysis by qPCR of patient mRNA showed an approximately 50% decrease in NAA10 mRNA compared to controls, whereas carrier females had similar levels to controls. RNAseq analysis of transcript structure in affected individuals revealed that read depth did not decrease as expected at the PAS in the 3-prime UTR, but declined approximately 600 bp further 3-prime at a predicted second PAS.


.0007   MICROPHTHALMIA, SYNDROMIC 1

NAA10, +39A-G, 3-PRIME UTR
SNP: rs1603289774, ClinVar: RCV001215737, RCV002264981

In a 5-generation family (family 2) with syndromic microphthalmia (MCOPS1; 309800), originally reported by Slavotinek et al. (2005), Johnston et al. (2019) identified a c.*39A-G transition (c.*39A-G, NM_003491.3) in the 3-prime UTR of the NAA10 gene (chrX:153,195,401T-C, GRCh37), altering the consensus polyadenylation sequence (PAS) from AATAAA to GATAAA. The mutation segregated with disease in the family. Three carrier females showed greater than 90% skewing of X inactivation, but the authors noted that females did not show consistent skewing of X inactivation. Analysis by qPCR of patient mRNA showed an approximately 50% decrease in NAA10 mRNA compared to controls, whereas carrier females had similar levels to controls. RNAseq analysis of transcript structure in affected individuals revealed that read depth did not decrease as expected at the PAS in the 3-prime UTR, but declined approximately 600 bp further 3-prime at a predicted second PAS.


.0008   MICROPHTHALMIA, SYNDROMIC 1

NAA10, +40A-G, 3-PRIME UTR
SNP: rs1342269961, ClinVar: RCV001215739, RCV001840731

In an 8-month-old boy (family 3) with syndromic microphthalmia (MCOPS1; 309800), Johnston et al. (2019) identified a c.*40A-G transition (c.*40A-G, NM_003491.3) in the 3-prime UTR of the NAA10 gene (chrX:153,195,400T-C, GRCh37), altering the consensus polyadenylation sequence (PAS) from AATAAA to AGTAAA. The mutation was present in his unaffected carrier mother.


.0009   MICROPHTHALMIA, SYNDROMIC 1

NAA10, 4-BP DEL
SNP: rs2148534324, ClinVar: RCV001375494, RCV002293532

In an 11-year-old boy (patient 23) with syndromic microphthalmia-1 (MCOPS1; 309800), Cheng et al. (2019) identified a 4-bp deletion (c.455_458del) in the NAA10 gene, resulting in a frameshift and premature termination (Thr152ArgfsTer6). The mutation was inherited from his mother.


.0010   OGDEN SYNDROME

NAA10, ARG83CYS
ClinVar: RCV000190675, RCV000225365, RCV000255490, RCV001257765, RCV002252040, RCV003401042

In 6 unrelated females and a brother-sister pair with Ogden syndrome (OGDNS; 300855), Saunier et al. (2016) identified heterozygosity or hemizygosity for a c.247C-T transition (c.247C-T, NM_003491.3) in the NAA10 gene, resulting in an arg83-to-cys (R83C) substitution. The mutations, which were found by trio whole-exome sequencing or by sequencing of a panel of genes associated with intellectual disability, were de novo in the 11 unrelated females and were due to maternal germline mosaicism in the sib pair. In vitro assays of mutant NAA10 with the R83C mutation demonstrated reduced catalytic activity and a higher Km compared to wildtype, indicating reduced affinity to acetyl-CoA.

In 11 unrelated females with OGDNS, Cheng et al. (2019) identified a de novo heterozygous c.247C-T transition in exon 5 of the NAA10 gene, resulting in an R83C substitution. The mutation was found by exome sequencing; it was not present in the gnomAD database. In vitro functional expression studies indicated that the mutation may have increased activity compared to wildtype in certain circumstances.

In an 18-year-old woman with OGDNS, Maini et al. (2021) identified heterozygosity for the R83C mutation in the NAA10 gene. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was shown to be de novo.


.0011   OGDEN SYNDROME

NAA10, PHE128LEU
ClinVar: RCV000225366, RCV000414068

In 2 unrelated female patients (patients 3 and 4) with Ogden syndrome (OGDNS; 300855), Saunier et al. (2016) identified a de novo heterozygous c.384T-A transversion (c.384T-A, NM_003491.3) in the NAA10 gene, resulting in a phe128-to-leu (F128L) substitution. The mutation was found by trio whole-exome sequencing and confirmed by Sanger sequencing. In vitro assays of mutant NAA10 with the F128L mutation demonstrated reduced protein stability.


.0012   OGDEN SYNDROME

NAA10, ARG79CYS
SNP: rs1057524031, ClinVar: RCV000436076, RCV000851511, RCV001305870, RCV001730682

In 2 brothers (individuals 4 and 5) and a maternal uncle (individual 3) with Ogden syndrome (OGDNS; 300855), McTiernan et al. (2022) identified a c.235C-T transition (c.235C-T, NM_003491.4) in the NAA10 gene, resulting in an arg79-to-cys (R79C) substitution. The mutation was identified by whole-exome sequencing. Another maternal uncle (individual 2) was similarly affected but did not undergo molecular testing. In vitro studies of NAA10 with the R79C mutation had reduced Nt-acetylation catalytic activity towards a synthetic oligopeptide compared to wildtype NAA10.


REFERENCES

  1. Arnesen, T., Anderson, D., Baldersheim, C., Lanotte, M., Varhaug, J. E., Lillehaug, J. R. Identification and characterization of the human ARD1-NATH protein acetyltransferase complex. Biochem. J. 386: 433-443, 2005. [PubMed: 15496142] [Full Text: https://doi.org/10.1042/BJ20041071]

  2. Asaumi, M., Iijima, K., Sumioka, A., Iijima-Ando, K., Kirino, Y., Nakaya, T., Suzuki, T. Interaction of N-terminal acetyltransferase with the cytoplasmic domain of beta-amyloid precursor protein and its effect on A-beta secretion. J. Biochem. 137: 147-155, 2005. [PubMed: 15749829] [Full Text: https://doi.org/10.1093/jb/mvi014]

  3. Bilton, R., Mazure, N., Trottier, E., Hattab, M., Dery, M.-A., Richard, D. E., Pouyssegur, J., Brahimi-Horn, M. C. Arrest-defective-1 protein, an acetyltransferase, does not alter stability of hypoxia-inducible factor (HIF)-1-alpha and is not induced by hypoxia or HIF. J. Biol. Chem. 280: 31132-31140, 2005. Note: Erratum: J. Biol. Chem. 281: 15592 only, 2006. [PubMed: 15994306] [Full Text: https://doi.org/10.1074/jbc.M504482200]

  4. Casey, J. P., Stove, S. I., McGorrian, C., Galvin, J., Blenski, M., Dunne, A., Ennis, S., Brett, F., King, M. D., Arnesen, T., Lynch, S. A. NAA10 mutation causing a novel intellectual disability syndrome with long QT due to N-terminal acetyltransferase impairment. Sci. Rep. 5: 16022, 2015. Note: Electronic Article. [PubMed: 26522270] [Full Text: https://doi.org/10.1038/srep16022]

  5. Cheng, H., Gottlieb, L., Marchi, E., Kleyner, R., Bhardwaj, P., Rope, A. F., Rosenheck, S., Moutton, S., Philippe, C., Eyaid, W., Alkuraya, F. S., Toribio, J., and 17 others. Phenotypic and biochemical analysis of an international cohort of individuals with variants in NAA10 and NAA15. Hum. Molec. Genet. 28: 2900-2919, 2019. Note: Erratum: Hum. Molec. Genet. 29: 877-878, 2020. [PubMed: 31127942] [Full Text: https://doi.org/10.1093/hmg/ddz111]

  6. Esmailpour, T., Riazifar, H., Liu, L., Donkervoort, S., Huang, V. H., Madaan, S., Shoucri, B. M., Busch, A., Wu, J., Towbin, A., Chadwick, R. B., Sequeira, A., Vawter, M. P., Sun, G., Johnston, J. J., Biesecker, L. G., Kawaguchi, R., Sun, H., Kimonis, V., Huang, T. A splice donor mutation in NAA10 results in the dysregulation of the retinoic acid signalling pathway and causes Lenz microphthalmia syndrome. J. Med. Genet. 51: 185-196, 2014. [PubMed: 24431331] [Full Text: https://doi.org/10.1136/jmedgenet-2013-101660]

  7. Forrester, S., Kovach, M. J., Reynolds, N. M., Urban, R., Kimonis, V. Manifestations in four males with and an obligate carrier of the Lenz microphthalmia syndrome. Am. J. Med. Genet. 98: 92-100, 2001. [PubMed: 11426460]

  8. Graham, C. A., McCleary, B. G., Malcolm, S., Kelly, E. D., Hill, A. J., Johnston, W. P., Nevin, N. C. Linkage analysis in a family with X-linked anophthalmos. (Abstract) J. Med. Genet. 25: 643 only, 1988.

  9. Graham, C. A., Redmond, R. M., Nevin, N. C. X-linked clinical anophthalmos: localization of the gene to Xq27-Xq28. Ophthalmic Paediat. Genet. 12: 43-48, 1991. [PubMed: 1679229] [Full Text: https://doi.org/10.3109/13816819109023084]

  10. Jeong, J.-W., Bae, M.-K., Ahn, M.-Y., Kim, S.-H., Sohn, T.-K., Bae, M.-H., Yoo, M.-A., Song, E. J., Lee, K.-J., Kim, K.-W. Regulation and destabilization of HIF-1-alpha by ARD1-mediated acetylation. Cell 111: 709-720, 2002. [PubMed: 12464182] [Full Text: https://doi.org/10.1016/s0092-8674(02)01085-1]

  11. Jeppesen, P., Turner, B. M. The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74: 281-289, 1993. [PubMed: 8343956] [Full Text: https://doi.org/10.1016/0092-8674(93)90419-q]

  12. Johnston, J. J., Williamson, K. A., Chou, C. M., Sapp, J. C., Ansari, M., Chapman, H. M., Cooper, D. N., Dabib, T., Dudley, J. N., Holt, R. J., Ragge, N. K., Schaffer, A. A., Sen, S. K., Slavotinek, A. M., FitzPatrick, D. R., Glaser, T. M., Stewart, F., Black, G. C. M., Biesecker, L. G. NAA10 polyadenylation signal variants cause syndromic microphthalmia. J. Med. Genet. 56: 444-453, 2019. [PubMed: 30842225] [Full Text: https://doi.org/10.1136/jmedgenet-2018-105836]

  13. Kim, S.-H., Park, J. A., Kim, J. H., Lee, J.-W., Seo, J. H., Jung, B.-K., Chun, K.-H., Jeong, J.-W., Bae, M.-K., Kim, K.-W. Characterization of ARD1 variants in mammalian cells. Biochem. Biophys. Res. Commun. 340: 422-427, 2006. [PubMed: 16376303] [Full Text: https://doi.org/10.1016/j.bbrc.2005.12.018]

  14. Maini, I., Caraffi, S. G., Peluso, F., Valeri, L., Nicoli, D., Laurie, S., Baldo, C., Zuffardi, O., Garavelli, L. Clinical Manifestations in a girl with NAA10-related syndrome and genotype-phenotype correlation in females. Genes (Basel) 12: 900, 2021. [PubMed: 34200686] [Full Text: https://doi.org/10.3390/genes12060900]

  15. McTiernan, N., Tranebjaerg, L., Bjorheim, A. S., Hogue, J. S., Wilson, W. G., Schmidt, B., Boerrigter, M. M., Nybo, M. L., Smeland, M. F., Tumer, Z., Arnesen, T. Biochemical analysis of novel NAA10 variants suggests distinct pathogenic mechanisms involving impaired protein N-terminal acetylation. Hum. Genet. 141: 1355-1369, 2022. [PubMed: 35039925] [Full Text: https://doi.org/10.1007/s00439-021-02427-4]

  16. Myklebust, L. M., Van Damme, P., Stove, S. I., Dorfel, M. J., Abboud, A., Kalvik, T. V., Grauffel, C., Jonckheere, V., Wu, Y., Swensen, J., Kaasa, H., Liszczak, G., Marmorstein, R., Reuter, N., Lyon, G. J., Gevaert, K., Arnesen, T. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Hum. Molec. Genet. 24: 1956-1976, 2015. [PubMed: 25489052] [Full Text: https://doi.org/10.1093/hmg/ddu611]

  17. Popp, B., Stove, S. I., Endele, S., Myklebust, L. M., Hoyer, J., Sticht, H., Azzarello-Burri, S., Rauch, A., Arnesen, T., Reis, A. De novo missense mutations in the NAA10 gene cause severe non-syndromic developmental delay in males and females. Europ. J. Hum. Genet. 23: 602-609, 2015. [PubMed: 25099252] [Full Text: https://doi.org/10.1038/ejhg.2014.150]

  18. Rauch, A., Wieczorek, D., Graf, E., Wieland, T., Endele, S., Schwarzmayr, T., Albrecht, B., Bartholdi, D., Beygo, J., Di Donato, N., Dufke, A., Cremer, K., and 27 others. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380: 1674-1682, 2012. [PubMed: 23020937] [Full Text: https://doi.org/10.1016/S0140-6736(12)61480-9]

  19. Rope, A. F., Wang, K., Evjenth, R., Xing, J., Johnston, J. J., Swensen, J. J., Johnson, W. E., Moore, B., Huff, C. D., Bird, L. M., Carey, J. C., Opitz, J. M., and 16 others. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am. J. Hum. Genet. 89: 28-43, 2011. Note: Erratum: Am. J. Hum. Genet. 89: 345 only, 2011. [PubMed: 21700266] [Full Text: https://doi.org/10.1016/j.ajhg.2011.05.017]

  20. Sanchez-Puig, N., Fersht, A. R. Characterization of the native and fibrillar conformation of the human N-alpha-acetyltransferase ARD1. Protein Sci. 15: 1968-1976, 2006. [PubMed: 16823041] [Full Text: https://doi.org/10.1110/ps.062264006]

  21. Saunier, C., Stove, S. I., Popp, B., Gerard, B., Blenski, M., AhMew, N., de Bie, C., Goldenberg, P., Isidor, B., Keren, B., Leheup, B., Lampert, L., and 19 others. Expanding the phenotype associated with NAA10-related N-terminal acetylation deficiency. Hum. Mutat. 37: 755-64, 2016. [PubMed: 27094817] [Full Text: https://doi.org/10.1002/humu.23001]

  22. Slavotinek, A., Lee, S. S., Hamilton, S. P. A family with X-linked anophthalmia: exclusion of SOX3 as a candidate gene. Am. J. Med. Genet. 138A: 89-94, 2005. [PubMed: 16114045] [Full Text: https://doi.org/10.1002/ajmg.a.30872]

  23. Sugiura, N., Adams, S. M., Corriveau, R. A. An evolutionarily conserved N-terminal acetyltransferase complex associated with neuronal development. J. Biol. Chem. 278: 40113-40120, 2003. [PubMed: 12888564] [Full Text: https://doi.org/10.1074/jbc.M301218200]

  24. Tribioli, C., Mancini, M., Plassart, E., Bione, S., Rivella, S., Sala, C., Torri, G., Toniolo, D. Isolation of new genes in distal Xq28: transcriptional map and identification of a human homologue of the ARD1 N-acetyltransferase of Saccharomyces cerevisiae. Hum. Molec. Genet. 3: 1061-1067, 1994. [PubMed: 7981673] [Full Text: https://doi.org/10.1093/hmg/3.7.1061]

  25. Whiteway, M., Szostak, J. W. The ARD1 gene of yeast functions in the switch between the mitotic cell cycle and alternative developmental pathways. Cell 43: 483-492, 1985. [PubMed: 3907857] [Full Text: https://doi.org/10.1016/0092-8674(85)90178-3]


Contributors:
Hilary J. Vernon - updated : 09/08/2022
Cassandra L. Kniffin - updated : 06/17/2021
Carol A. Bocchini - updated : 04/26/2021
Marla J. F. O'Neill - updated : 07/10/2020
Marla J. F. O'Neill - updated : 07/10/2020
Patricia A. Hartz - updated : 10/28/2016
Cassandra L. Kniffin - updated : 11/23/2015
Marla J. F. O'Neill - updated : 1/29/2014
Ada Hamosh - updated : 8/19/2011
Patricia A. Hartz - updated : 3/6/2007
Stefanie A. Nelson - updated : 2/22/2007
Stylianos E. Antonarakis - updated : 1/17/2003

Creation Date:
Victor A. McKusick : 2/4/1996

Edit History:
carol : 09/09/2022
carol : 09/08/2022
carol : 11/10/2021
alopez : 07/07/2021
ckniffin : 06/17/2021
carol : 05/05/2021
carol : 04/26/2021
alopez : 07/10/2020
alopez : 07/10/2020
carol : 10/20/2017
carol : 08/24/2017
alopez : 06/28/2017
alopez : 10/28/2016
carol : 11/24/2015
ckniffin : 11/23/2015
mcolton : 8/7/2014
carol : 1/29/2014
mcolton : 1/28/2014
carol : 12/20/2011
carol : 9/13/2011
alopez : 9/12/2011
alopez : 8/24/2011
alopez : 8/24/2011
terry : 8/19/2011
carol : 7/6/2011
alopez : 6/17/2010
wwang : 3/6/2007
wwang : 2/22/2007
ckniffin : 8/3/2005
ckniffin : 3/23/2004
mgross : 1/17/2003
mgross : 1/17/2003
joanna : 8/31/1998
joanna : 8/31/1998
joanna : 2/4/1996
joanna : 2/4/1996