Alternative titles; symbols
HGNC Approved Gene Symbol: SRCAP
SNOMEDCT: 312214005;
Cytogenetic location: 16p11.2 Genomic coordinates (GRCh38) : 16:30,699,171-30,741,409 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 16p11.2 | Developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities | 619595 | Autosomal dominant | 3 |
| Floating-Harbor syndrome | 136140 | Autosomal dominant | 3 |
The SRCAP gene encodes a core catalytic component of the multiprotein SRCAP chromatin-remodeling complex, which regulates transcription of various target genes by incorporating H2A.Z-H2B dimers into nucleosomes (summary by Rots et al., 2021).
By sequencing clones obtained from a size-fractionated brain cDNA library, Nagase et al. (1997) cloned SRCAP, which they designated KIAA0309. RT-PCR detected low to moderate expression in most tissues examined.
Using the transcription coactivation domain of CBP (CREBBP; 600140) as bait in a yeast 2-hybrid of a HeLa cell cDNA library, followed by screening a human SKN plasmid library, Johnston et al. (1999) cloned SRCAP. The deduced 2,971-amino acid protein has a calculated molecular mass of 315 kD. It has a highly charged N-terminal domain, a central CBP-binding domain, a second charged domain, and a putative C-terminal DNA-binding domain. A complete ATPase domain, consisting of 7 highly conserved regions, are dispersed over the length of the protein.
By radiation hybrid analysis, Nagase et al. (1997) mapped the SRCAP gene to chromosome 16.
Stumpf (2021) mapped the SRCAP gene to chromosome 16p11.2 based on an alignment of the SRCAP sequence (GenBank AF143946) with the genomic sequence (GRCh38).
Johnston et al. (1999) showed that SRCAP increased transcription of a reporter plasmid when it was cotransfected with the transcription activation domain of CBP. Endogenous SRCAP immunoprecipitated from nuclear extracts of a human lung epithelial cell line had ATPase activity, and the C-terminal half of SRCAP enhanced the ability of CBP to activate transcription. Adenovirus protein E1A blocked the ability of CBP to function as a coactivator for a number of transcription factors. Johnston et al. (1999) showed that binding of E1A to CBP excluded binding of SRCAP to CBP, suggesting a means by which E1A represses the coactivator function of CBP.
Adenovirus DNA-binding protein (Dbp) is a multifunctional protein involved in several aspects of the adenovirus life cycle, including an ability to modulate transcription. Xu et al. (2001) showed that in vitro-translated Dbp and SRCAP proteins interacted and that Dbp inhibited SRCAP transcriptional activity in a dose-dependent manner.
Monroy et al. (2003) stated that SRCAP is found in multiprotein complexes that include proteins found in SWI/SNF (see SMARCA2; 600014) chromatin remodeling complexes. They demonstrated that SRCAP enhanced phosphoenolpyruvate carboxykinase (see PCK1; 261680) promoter transcription induced by glucocorticoids. SRCAP also enhanced glucocorticoid receptor (GCCR; 138040)-mediated transcription of a simple promoter containing only 2 glucocorticoid response elements. SRCAP served as a coactivator of the androgen receptor (313700) and exhibited synergistic activation with nuclear receptor coactivators and functionally interacted in vivo with glucocorticoid receptor-interacting protein-1 (NCOA2; 601993) and coactivator-associated arginine methyltransferase-1 (CARM1; 603934). Monroy et al. (2003) proposed that SRCAP, by virtue of its ability to interact with CBP, functions as a coactivator to regulate transcription initiated by several signaling pathways.
Eissenberg et al. (2005) stated that the SRCAP homolog in Drosophila is the domino (Dom) gene. They showed that human SRCAP complemented recessive domino-mutant phenotypes, and the rescue depended on an intact ATPase homology domain. SRCAP colocalized with Dom on Drosophila polytene chromosomes and was recruited to sites of active transcription, such as steroid-regulated loci, but not to activated heat shock loci. SCCAP recruited Drosophila Cbp to ectopic chromosomal sites, suggesting that SRCAP and Cbp interacted directly or indirectly on chromosomes. They showed that Dom is a Notch (190198) pathway activator in Drosophila and that wildtype SRCAP, but not an ATPase domain mutant, substituted for Dom in Notch-dependent wing development. SRCAP also potentiated Notch-dependent gene activation in HeLa cells.
By chromatin immunoprecipitation analysis of a human lung carcinoma cell line, Wong et al. (2007) found that SRCAP was recruited to both active and inactive promoters, with highest levels of SRCAP on the active SP1 (189906), G3BP (608431), and FAD synthetase (FLAD1; 610595) promoters. The sites of SRCAP recruitment on these promoters overlapped or occurred adjacent to the sites of deposition of H2AZ (142763) and acetylated H2AZ. Knockdown of SRCAP expression resulted in decreased deposition of H2AZ and acetylated H1AZ and decreased levels of SP1, G3BP, and FAD synthetase mRNA. Wong et al. (2007) concluded that SRCAP mediates in vivo deposition of H2AZ.
INO80 (see 610169) and SWRC are multisubunit complexes that catalyze the deposition and removal, respectively, of histone variant H2AZ from the first nucleosome at the start of genes. Using ultra-high resolution mapping of protein-genome interactions, Yen et al. (2013) identified the subnucleosomal placement of 20 subunits of INO80 and SWRC across the yeast genome. The studies suggested that INO80 and SWRC engulf +1 nucleosomes in their entirety, with different subunits occupying specific positions (crosslinks) along the nucleosome in a manner that is similar for most +1 nucleosomes. Ino80, the catalytic subunit of INO80, crosslinked across much of the +1 nucleosome and showed moderately correlated cooccupancy with Swr1, its counterpart in SWRC.
Floating-Harbor Syndrome
In 13 unrelated patients with Floating-Harbor syndrome (FLHS; 136140), Hood et al. (2012) identified heterozygosity for 5 different truncating mutations in the SRCAP gene (see, e.g., 611421.0001-611421.0003), all of which were located in the final exon (exon 34) and were not represented in the dbSNP (build 131), 1000 Genomes Project, or NHLBI Exome Variant Server databases. The mutations were shown to be de novo in all 6 instances in which parental DNA was available. Hood et al. (2012) stated that given the structure of SRCAP, the nonrandom clustering of truncating mutations seen in these patients was strongly suggestive of a dominant-negative disease mechanism due to loss of one or more critical domains.
By whole-exome sequencing followed by Sanger sequencing, Le Goff et al. (2013) identified heterozygous de novo mutations in exon 34 of the SRCAP gene in 6 of 9 patients with Floating-Harbor syndrome (see, e.g., 611421.0001, 611421.0002, and 611421.0004). Le Goff et al. (2013) noted that these findings confirmed exon 34 as a mutation hotspot, and that the absence of an SRCAP mutation in 3 patients fulfilling all the characteristics of Floating-Harbor syndrome suggested genetic heterogeneity, although partial intragenic deletions or mutations in the introns or promoter region could not be excluded.
Nikkel et al. (2013) identified heterozygous truncating mutations in exon 34 of the SRCAP gene in 52 patients with FLHS. The most common mutations were R2444X (611421.0001), occurring in 24 individuals, followed by R2435X (611421.0002), found in 13 patients. The boundaries of the critical FHLS region were extended between codons 2389 and 2748. Functional studies of the variants and studies of patient cells were not performed.
In 5 unrelated patients with FLHS, Seifert et al. (2014) identified 5 de novo heterozygous truncating mutations in the SRCAP gene. One patient each carried the recurrent R2444X (patient C) and R2435X (patient D) mutations, 2 patients (patients A and B) carried novel frameshift mutations in exon 34 (see, e.g., 611421.0007), and 1 patient (patient E) carried a nonsense mutation in exon 33 (R2329X; 611421.0006). The mutations were found by sequencing the SRCAP gene, including flanking intronic sequences and the promoter region. Functional studies of the variants and studies of patient cells were not performed. The findings confirmed a hotspot for FHLS mutations in the final exons of the SRCAP gene that are predicted to lack the putative C-terminal AT-hook DNA binding motif. Seifert et al. (2014) noted that a dominant-negative mechanism for these mutations has been postulated, and suggested that truncating mutations outside of exons 33 and 34 may result in nonsense-mediated decay leading to different phenotypic consequences.
Developmental Delay, Hypotonia, Musculoskeletal Defects, And Behavioral Abnormalities
In 33 unrelated patients with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (DEHMBA; 619595), Rots et al. (2021) identified heterozygous truncating mutations in the SRCAP gene (see, e.g., 611421.0008-611421.0011). The mutations, which were found by exome sequencing, occurred de novo in those from whom parental DNA was available, which was the majority of patients. None of the mutations were present in the gnomAD database. The mutations occurred proximal to the FLHS region in 28 individuals and distal to the FLHS region in 5 individuals. None of the mutations was recurrent. DNA methylation (DNAm) analysis of 8 patients with FLHS, 9 with proximal SRCAP variants, and 5 with distal SRCAP variants showed distinct methylation signatures, suggesting diverse pathogenicity of these variants. Gene ontology analysis showed that signature CpGs mapped to genes relevant to SRCAP function, including those involved in chromosome structure, DNA repair, and DNA recombination. Rots et al. (2021) hypothesized that truncating mutations proximal to the FLHS region may be subject to nonsense-mediated mRNA decay and cause haploinsufficiency.
In 6 unrelated patients with Floating-Harbor syndrome (FLHS; 136140), 2 of whom were previously studied by White et al. (2010) (patients 9 and 10), Hood et al. (2012) identified heterozygosity for a 7330C-T transition in exon 34 of the SRCAP gene, resulting in an arg2444-to-ter (R2444X) substitution. The mutation was shown to be de novo in the 2 patients for whom parental DNA was available, and was not represented in the dbSNP (build 131), 1000 Genomes Project, or NHLBI Exome Variant Server databases.
In a 32-year-old French woman and a 28-year-old woman of Spanish and Portuguese ancestry with Floating-Harbor syndrome, Le Goff et al. (2013) identified heterozygosity for the R2444X mutation in the SRCAP gene. The mutation occurred de novo in both women and was not found in 200 control chromosomes.
In 4 unrelated patients with Floating-Harbor syndrome (FLHS; 136140), 1 of whom was previously studied by White et al. (2010) (patient 8), Hood et al. (2012) identified heterozygosity for a 7303C-T transition in exon 34 of the SRCAP gene, resulting in an arg2435-to-ter (R2435X) substitution. The mutation was shown to be de novo in the 1 patient for whom parental DNA was available, and was not represented in the dbSNP (build 131), 1000 Genomes Project, or NHLBI Exome Variant Server databases.
In a 7.5-year-old French boy with Floating-Harbor syndrome, Le Goff et al. (2013) identified heterozygosity for the R2435X mutation in the SRCAP gene. The mutation occurred de novo in the boy and was not found in 200 control chromosomes.
In a 4.25-year-old boy of German and Mexican descent with Floating-Harbor syndrome (FLHS; 136140), Hood et al. (2012) identified heterozygosity for a de novo 1-bp deletion (7549delC) in exon 34 of the SRCAP gene, causing a frameshift predicted to result in a premature termination codon. The mutation was not present in his unaffected parents and was not represented in the dbSNP (build 131), 1000 Genomes Project, or NHLBI Exome Variant Server databases.
In a 10-year-old French girl with Floating-Harbor syndrome (FHLS; 136140), Le Goff et al. (2013) identified heterozygosity for a de novo 1-bp duplication at nucleotide 7863 in exon 34 of the SRCAP gene, causing a frameshift predicted to result in a premature termination codon (Gln2622fsTer8). The mutation was not found in the girl's parents or in 200 control chromosomes.
In a German boy with Floating-Harbor syndrome (FLHS; 136140), Kehrer et al. (2014) identified a de novo heterozygous c.7000C-T transition in exon 33 of the SRCAP gene, resulting in a gln2334-to-ter (Q2334X) substitution. Kehrer et al. (2014) noted that this was the first reported SRCAP mutation that was not in exon 34. Functional studies were not performed.
In a 10-year-old girl (patient E) with Floating-Harbor syndrome (FLHS; 136140), Seifert et al. (2014) identified a de novo heterozygous c.6985C-T transition (c.6985C-T, NM_006662.2) in exon 33 of the SRCAP gene, resulting in an arg2329-to-ter (R2329X) substitution. The mutation was found by direct sequencing of the SRCAP gene. Functional studies of the variant and studies of patient cells were not performed. The patient had physical features of the disorder and had only mild speech delay and some behavioral problems; cognitive skills were normal and she was able to attend a normal school.
In a 22-year-old woman (patient B) with Floating-Harbor syndrome (FLHS; 136140), Seifert et al. (2014) identified a de novo heterozygous 1-bp duplication (c.7218dupT, NM_006662.2) in exon 34 of the SRCAP gene, resulting in a frameshift and premature termination (Gln2407SerfsTer36). The mutation was found by direct sequencing of the SRCAP gene. Functional studies of the variant and studies of patient cells were not performed. The patient had previously been reported by Wieczorek et al. (2001).
In a 36-year-old man (proximal patient 2) with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (DEHMBA; 619595) Rots et al. (2021) identified a heterozygous frameshift mutation in the SRCAP gene (c.1143_1153delinsTGT, NM_006662.3), resulting in premature termination (Pro382ValfsTer14). The mutation, which was found by exome sequencing, was not present in the gnomAD database. The mutation occurred proximal to the FLHS critical region. DNA methylation analysis of patient 2 showed a distinct signature compared to controls and to patients with FLHS, suggesting a unique pathogenetic mechanism. The patient had mild intellectual disability, autism spectrum disorder, ADHD, dysmorphic features, and congenital hip dysplasia.
In a 21-year-old man (proximal patient 11) with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (DEHMBA; 619595), Rots et al. (2021) identified a de novo heterozygous 4-bp deletion in the SRCAP gene (c.4557_4560del, NM_006662.3), resulting in premature termination (Gln1519HisfsTer18). The mutation, which was found by exome sequencing, was not present in the gnomAD database. The mutation occurred proximal to the FLHS critical region. DNA methylation analysis of patient 11 showed a distinct signature compared to controls and to patients with FLHS, suggesting a unique pathogenetic mechanism. The patient had learning disabilities, behavioral disorders, dysmorphic facial features, and joint hypermobility with musculoskeletal pain.
In an 18-year-old man (proximal patient 18) with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (DEHMBA; 619595), Rots et al. (2021) identified a de novo heterozygous 4-bp deletion (c.5977_5980del, NM_006662.3) in the SRCAP gene, resulting in a frameshift and premature termination (Cys1993ThrfsTer42). The mutation, which was found by exome sequencing, was not present in the gnomAD database. The mutation occurred proximal to the FLHS critical region. DNA methylation analysis of patient 18 showed a distinct signature compared to controls and to patients with FLHS, suggesting a unique pathogenetic mechanism. The patient had learning disabilities, behavioral disorders, and dysmorphic facial features.
In a 14-year-old girl (distal patient 5) with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (DEHMBA; 619595), Rots et al. (2021) identified a de novo heterozygous 1-bp deletion (c.9344del, NM_006662.3) in the SRCAP gene, resulting in a frameshift and premature termination (Pro3115GlnfsTer13). The mutation, which was found by exome sequencing, was not present in the gnomAD database. The mutation occurred distal to the FLHS critical region. DNA methylation analysis of patient 5 showed a distinct signature compared to controls and to patients with FLHS, suggesting a unique pathogenetic mechanism. The patient had mild intellectual disability and dysmorphic facial features.
Eissenberg, J. C., Wong, M., Chrivia, J. C. Human SRCAP and Drosophila melanogaster DOM are homologs that function in the Notch signaling pathway. Molec. Cell. Biol. 25: 6559-6569, 2005. [PubMed: 16024792] [Full Text: https://doi.org/10.1128/MCB.25.15.6559-6569.2005]
Hood, R. L., Lines, M. A., Nikkel, S. M., Schwartzentruber, J., Beaulieu, C., Nowaczyk, M. J. M., Allanson, J., Kim, C. A., Wieczorek, D., Moilanen, J. S., Lacombe, D., Gillessen-Kaesbach, G., and 17 others. Mutations in SRCAP, encoding SNF2-related CREBBP activator protein, cause Floating-Harbor syndrome. Am. J. Hum. Genet. 90: 308-313, 2012. [PubMed: 22265015] [Full Text: https://doi.org/10.1016/j.ajhg.2011.12.001]
Johnston, H., Kneer, J., Chackalaparampil, I., Yaciuk, P., Chrivia, J. Identification of a novel SNF2/SWI2 protein family member, SRCAP, which interacts with CREB-binding protein. J. Biol. Chem. 274: 16370-16376, 1999. [PubMed: 10347196] [Full Text: https://doi.org/10.1074/jbc.274.23.16370]
Kehrer, M., Beckmann, A., Wyduba, J., Finckh, U., Dufke, A., Gaiser, U., Tzschach, A. Floating-Harbor syndrome: SRCAP mutations are not restricted to exon 34. (Letter) Clin. Genet. 85: 498-499, 2014. [PubMed: 23763483] [Full Text: https://doi.org/10.1111/cge.12199]
Le Goff, C., Mahaut, C., Bottani, A., Doray, B., Goldenberg, A., Moncla, A., Odent, S., Nitschke, P., Munnich, A., Faivre, L., Cormier-Daire, V. Not all Floating-Harbor syndrome cases are due to mutations in exon 34 of SRCAP. Hum. Mutat. 34: 88-92, 2013. [PubMed: 22965468] [Full Text: https://doi.org/10.1002/humu.22216]
Monroy, M. A., Schott, N. M., Cox, L., Chen, J. D., Ruh, M., Chrivia, J. C. SNF2-related CBP activator protein (SRCAP) functions as a coactivator of steroid receptor-mediated transcription through synergistic interactions with CARM-1 and GRIP-1. Molec. Endocr. 17: 2519-2528, 2003. [PubMed: 14500758] [Full Text: https://doi.org/10.1210/me.2003-0208]
Nagase, T., Ishikawa, K., Nakajima, D., Ohira, M., Seki, N., Miyajima, N., Tanaka, A., Kotani, H., Nomura, N., Ohara, O. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. DNA Res. 4: 141-150, 1997. [PubMed: 9205841] [Full Text: https://doi.org/10.1093/dnares/4.2.141]
Nikkel, S. M., Dauber, A., de Munnik, S., Connolly, M., Hood, R. L., Caluseriu, O., Hurst, J., Kini, U., Nowaczyk, M. J. M., Afenjar, A., Albrecht, B., Allanson, J. E., and 57 others. The phenotype of Floating-Harbor syndrome: clinical characterization of 52 individuals with mutations in exon 34 of SRCAP. Orphanet J. Rare Dis. 8: 63, 2013. [PubMed: 23621943] [Full Text: https://doi.org/10.1186/1750-1172-8-63]
Rots, D., Chater-Diehl, E., Dingemans, A. J. M., Goodman, S. J., Siu, M. T., Cytrynbaum, C., Choufani, S., Hoang, N., Walker, S., Awamleh, Z., Charkow, J., Meyn, S., and 76 others. Truncating SRCAP variants outside the Floating-Harbor syndrome locus cause a distinct neurodevelopmental disorder with a specific DNA methylation signature. Am. J. Hum. Genet. 108: 1053-1068, 2021. [PubMed: 33909990] [Full Text: https://doi.org/10.1016/j.ajhg.2021.04.008]
Seifert, W., Meinecke, P., Kruger, G., Rossier, E., Heinritz, W., Wusthof, A., Horn, D. Expanded spectrum of exon 33 and 34 mutations in SRCAP and follow-up in patients with Floating-Harbor syndrome. BMC Med. Genet. 15: 127, 2014. [PubMed: 25433523] [Full Text: https://doi.org/10.1186/s12881-014-0127-0]
Stumpf, A. M. Personal Communication. Baltimore, Md. 11/08/2021.
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Wieczorek, D., Wusthof, A., Harms, E., Meinecke, P. Floating-Harbor syndrome in two unrelated girls: mild short stature in one patient and effective growth hormone therapy in the other. Am. J. Med. Genet. 104: 47-52, 2001. [PubMed: 11746027] [Full Text: https://doi.org/10.1002/ajmg.1585]
Wong, M. M., Cox, L. K., Chrivia, J. C. The chromatin remodeling protein, SRCAP, is critical for deposition of the histone variant H2A.Z at promoters. J. Biol. Chem. 282: 26132-26139, 2007. [PubMed: 17617668] [Full Text: https://doi.org/10.1074/jbc.M703418200]
Xu, X., Chackalaparampil, I., Monroy, M. A., Cannella, M. T., Pesek, E., Chrivia, J., Yaciuk, P. Adenovirus DNA binding protein interacts with the SNF2-related CBP activator protein (SrCap) and inhibits SrCap-mediated transcription. J. Virol. 75: 10033-10040, 2001. [PubMed: 11581372] [Full Text: https://doi.org/10.1128/JVI.75.21.10033-10040.2001]
Yen, K., Vinayachandran, V., Pugh, B. F. SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell 154: 1246-1256, 2013. [PubMed: 24034248] [Full Text: https://doi.org/10.1016/j.cell.2013.08.043]