Alternative titles; symbols
HGNC Approved Gene Symbol: PHYH
Cytogenetic location: 10p13 Genomic coordinates (GRCh38) : 10:13,277,799-13,300,064 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 10p13 | Refsum disease | 266500 | Autosomal recessive | 3 |
The PHYH gene encodes phytanoyl-CoA hydroxylase, a peroxisomal protein that catalyzes the first step in the alpha-oxidation of phytanic acid, a branched-chain fatty acid. Because beta-oxidation is blocked by the methyl group at C-3, phytanic acid must first undergo decarboxylation via an alpha-oxidation mechanism catalyzed by PHYH (Jansen et al., 1997).
The gene encoding the PHYH enzyme was identified by Mihalik et al. (1997) starting from studies of peroxisomal genes and gene defects in yeast and independently by Jansen et al. (1997) working back from the partial amino acid sequence of the purified rat protein. Both groups made use of expressed sequence tag (EST) database searching for identification of the full-length human cDNA sequence. The open reading frame encodes a 41.2-kD protein of 338 amino acids, which contains a cleavable peroxisomal targeting signal type 2 (PTS2).
Jansen et al. (2000) determined that the PHYH gene spans approximately 21 kb and contains 9 exons.
Radiation hybrid data studies by Mihalik et al. (1997) placed the PAHX gene on chromosome 10 between markers D10S249 and D10S466.
The structure and subcellular localization of the phytanic acid alpha-oxidation pathway long remained enigmatic, although it was generally assumed to involve phytanic acid and not its CoA-ester. However, this view was challenged by the finding in rat liver that phytanic acid must first be activated to its CoA ester, phytanoyl-CoA, before it can be oxidized (Watkins et al., 1994).
Mihalik et al. (1995) identified an enzyme activity (phytanoyl-CoA hydroxylase) in rat-liver peroxisomes by which phytanoyl-CoA is converted to 2-hydroxyphytanoyl-CoA. Jansen et al. (1996) showed that phytanoyl-CoA hydroxylase is present in human liver. Furthermore, they showed that it is located in peroxisomes and is deficient in liver from Zellweger syndrome (see 214100) patients, who lack morphologically distinguishable peroxisomes, providing an explanation for the long-known deficient oxidation of phytanic acid in these patients. They also showed that phytanic acid alpha-oxidation is peroxisomal and that it utilizes the CoA derivative as substrate, thus giving support in favor of the revised pathway of phytanic acid alpha-oxidation.
Mihalik et al. (1997) found that human PAHX is targeted to peroxisomes, requires the PTS2 receptor PEX7 (601757) for peroxisomal localization, interacts with the PTS2 receptor in the yeast 2-hybrid assay, and has intrinsic phytanoyl-CoA alpha-hydroxylase activity that requires the dioxygenase cofactor iron and cosubstrate 2-oxoglutarate.
Using the yeast 2-hybrid system to investigate the physiologic function of FKBP52 (600611), Chambraud et al. (1999) found that PAHX is an FKBP-associated protein. They found, furthermore, that the protein corresponds to the mouse protein Lnap1, which, based on studies of the MRL/lpr mouse, may be involved in the progression of lupus nephritis (Iwano et al., 1996). Chambraud et al. (1999) suggested that PAHX is a serious candidate for studying the cellular signaling pathway(s) involving FKBP52 in the presence of immunosuppressant drugs.
McDonough et al. (2005) stated that both the pro and mature forms of human PAHX are enzymatically active and show similar substrate specificity.
McDonough et al. (2005) solved the x-ray crystallographic structure of human PAHX complexed with Fe(2+) and 2-oxoglutarate to 2.5-angstrom resolution. PAHX has a double-stranded beta-helix core with 3 iron-binding residues, his175, asp177, and his264. The 2-oxoacid group of 2-oxoglutarate binds to Fe(2+) in a bidentate manner. Cys191 is positioned 6.7-angstrom from Fe(2+), and his155 and his281 form part of the active site. Of the 15 PAHX residues identified in Refsum disease (266500) patients, 11 cluster in 2 distinct groups around the binding sites for Fe(2+) (e.g., gln176; see 602026.0007) and 2-oxoglutarate (e.g., gly204; see 602026.0008).
Mihalik et al. (1997) and Jansen et al. (1997) identified homozygous or compound heterozygous mutations in the PHYH gene (602026.0001-602026.0004) in a total of 7 patients with Refsum disease (266500).
In 22 patients with Refsum disease, Jansen et al. (2000) identified mutations in the PHYH gene, including 14 different missense mutations, a 3-bp insertion, and a 1-bp deletion, which were all confirmed at the genome level. A 111-bp deletion identified in the PHYH cDNA of several patients with Refsum disease was due to either 1 of 2 different mutations in the same splice acceptor site (e.g., see 602026.0002), which result in skipping of exon 3. Six mutations were expressed in S. cerevisiae, and all led to an enzymatically inactive PhyH protein.
Mukherji et al. (2001) relied on crystallographic data for other members of the 2-oxoglutarate-dependent oxygenase superfamily to generate secondary structural predictions for the PHYH gene, which were tested by site-directed mutagenesis. Constructed H175A and D177A mutants did not catalyze hydroxylation of phytanoyl-CoA, consistent with the assigned role of these residues as iron(II) binding ligands. The clinically observed mutations pro29 to ser (P29S; 602026.0006), gln176 to lys (Q176K; 602026.0007), gly204 to ser (G204S; 602026.0008), asn269 to his (N269H; 602026.0004), arg275 to gln (R275Q; 602026.0009), and arg275 to trp (R275W; 602026.0001) were assayed for both 2-oxoglutarate and phytanoyl-CoA oxidation. The P29S mutant was fully active, implying that the mutation may result in defective targeting of the protein to peroxisomes. Mutation of arg275 resulted in impaired 2-oxoglutarate binding. The Q176K, G204S, and N269H mutations caused partial uncoupling of 2-oxoglutarate conversion from phytanoyl-CoA oxidation. The authors cautioned that the diagnosis of Refsum disease should not solely rely upon PHYH assays for 2-oxoglutarate or phytanoyl-CoA oxidation.
Jansen et al. (2004) reviewed mutations in the PHYH gene causing Refsum disease.
In a Ukrainian patient with Refsum disease (266500), whose parents originated from the same region, Mihalik et al. (1997) identified a homozygous 823C-T transition in the PHYH gene, predicted to result in an arg275-to-trp (R275W) amino acid substitution. The mutation also eliminated a unique BspEI restriction site. The arginine-275 residue is conserved in both the mouse and the C. elegans forms of the protein. In vitro functional expression studies showed that the mutant enzyme was inactive.
Jansen et al. (2000) expressed the mutant R275W allele in S. cerevisiae and determined that no enzymatic activity was present.
In a patient with Refsum disease (266500), Mihalik et al. (1997) discovered a truncated form of PHYH mRNA lacking 111 nucleotides of the open reading frame (residues 158-269 of the cDNA sequence), deleting codons 46-82. (Jansen et al. (1997) stated that this nucleotide numbering was incorrect; see below.) Sequence analysis of genomic DNA spanning this region of the gene revealed the absence of a single exon in the cDNA. An A-to-G transition was found at the penultimate residue of the upstream intron, altering the consensus splice acceptor sequence of AG to GG. The patient was homozygous for the mutation.
In 3 unrelated patients with Refsum disease, Jansen et al. (2000) identified a homozygous splice site mutation, IVS-2A-G, causing a 111-bp deletion comprising exon 3 (c.135-246del). The deletion did not cause a frameshift, but resulted in a protein lacking 37 internal amino acids (Tyr46-Arg82del) that was presumed to be enzymatically inactive.
In a brother and sister with Refsum disease (266500), born to healthy first-cousin Pakistani parents, Jansen et al. (1997) identified a homozygous deletion of nucleotide 164T in the PHYH gene, leading to a frameshift and a premature stop codon after amino acid 66. The first manifestation in the sister was nystagmus at the age of 6 months. Night blindness and retinitis pigmentosa were found at the age of 8 years. At the age of 10 years, she had ataxia, deafness, ichthyosis, and short metacarpal bones, as well as peripheral neuropathy but normal intellectual performance. Plasma phytanic acid level was elevated. The brother showed elevated plasma phytanic acid when first measured at 7 weeks. He was placed on a low phytanic acid diet with vitamin C supplement. His development was good and he appeared to see well. Although the appearance of his retina was normal, visual evoked responses were delayed and ERG response was poor.
In a Caucasian male with Refsum disease (266500) reported by Skjeldal et al. (1987), Jansen et al. (1997) identified a heterozygous 805A-C transversion in the PHYH gene, resulting in an asn269-to-his (N269H) substitution. The patient was a compound heterozygote for this missense mutation and for a 111-bp deletion (602026.0002), which was observed in 2 other unrelated patients.
In 2 sibs with Refsum disease (266500), Jansen et al. (2000) demonstrated homozygosity for a 3-bp insertion (576insGCC) in exon 6 of the PHYH gene, resulting in addition of an alanine residue after amino acid 192.
This variant, formerly titled REFSUM DISEASE, ADULT, 1, has been reclassified as a polymorphism. As of December 2012, the pro29-to-ser (P29S) variant had an overall population frequency of 20% (Exome Variant Server, 2012). In addition, the patients reported by Jansen et al. (2000) with this mutation had additional mutations in the PHYH gene that may have been causative and the P29S mutant was found to be fully active.
In 2 patients (patients 1 and 2) with Refsum disease (266500), Jansen et al. (2000) found an 85C-T transition in the PHYH gene, leading to a P29S substitution. The patients also had a truncating mutation (602026.0002) and either 589G-C or 648C-T leading to missense mutations E197Q or H220Y, respectively. Patient 2 also had 526C-A transversion leading to a Q176K (602026.0007) substitution.
In the cDNA of a patient (patient 2) with Refsum disease (266500), Jansen et al. (2000) identified mutations in the PHYH gene: a 526C-A transversion, leading to a gln176-to-lys (Q176K) substitution, and a truncating mutation (602026.0002). The patient also had a P29S polymorphism (602026.0006) and a 589G-C transversion, leading to a glu197-to-gln (E197Q) substitution.
In the cDNA of a patient (patient 10) with Refsum disease (266500), Jansen et al. (2000) identified homozygosity for a 610G-A transition in the PHYH gene, leading to a gly204-to-ser (G204S) substitution.
In the cDNA of a patient (patient 15) with Refsum disease (266500), Jansen et al. (2000) identified homozygosity for an 824G-A transition in the PHYH gene, resulting in an arg275-to-gln (R275Q) substitution.
Chambraud, B., Radanyi, C., Camonis, J. H., Rajkowski, K., Schumacher, M., Baulieu, E.-E. Immunophilins, Refsum disease, and lupus nephritis: the peroxisomal enzyme phytanoyl-COA alpha-hydroxylase is a new FKBP-associated protein. Proc. Nat. Acad. Sci. 96: 2104-2109, 1999. [PubMed: 10051602] [Full Text: https://doi.org/10.1073/pnas.96.5.2104]
Exome Variant Server. NHLBI GO Exome Sequencing Project (ESP), Seattle, WA. http://evs.gs.washington.edu/EVS 12/2012.
Iwano, M., Ueno, S., Miyazaki, M., Harada, T., Nagai, Y., Hirano, M., Dohi, Y., Akai, Y., Kurioka, H., Dohi, K. Molecular cloning and expression of a novel peptide (LN1) gene: reduced expression in the renal cortex of lupus nephritis in MRL/lpr mouse. Biochem. Biophys. Res. Commun. 229: 355-360, 1996. [PubMed: 8954131] [Full Text: https://doi.org/10.1006/bbrc.1996.1805]
Jansen, G. A., Hogenhout, E. M., Ferdinandusse, S., Waterham, H. R., Ofman, R., Jakobs, C., Skjeldal, O. H., Wanders, R. J. A. Human phytanoyl-CoA hydroxylase: resolution of the gene structure and the molecular basis of Refsum's disease. Hum. Molec. Genet. 9: 1195-1200, 2000. [PubMed: 10767344] [Full Text: https://doi.org/10.1093/hmg/9.8.1195]
Jansen, G. A., Mihalik, S. J., Watkins, P. A., Moser, H. W., Jakobs, C., Denis, S., Wanders, R. J. A. Phytanoyl-CoA hydroxylase is present in human liver, located in peroxisomes, and deficient in Zellweger syndrome: direct, unequivocal evidence for the new, revised pathway of phytanic acid alpha-oxidation in humans. Biochem. Biophys. Res. Commun. 229: 205-210, 1996. [PubMed: 8954107] [Full Text: https://doi.org/10.1006/bbrc.1996.1781]
Jansen, G. A., Ofman, R., Ferdinandusse, S., Ijlst, L., Muijsers, A. O., Skjeldal, O. H., Stokke, O., Jakobs, C., Besley, G. T. N., Wraith, J. E., Wanders, R. J. A. Refsum disease is caused by mutations in the phytanoyl-CoA hydroxylase gene. Nature Genet. 17: 190-193, 1997. [PubMed: 9326940] [Full Text: https://doi.org/10.1038/ng1097-190]
Jansen, G. A., Waterham, H. R., Wanders, R. J. A. Molecular basis of Refsum disease: sequence variations in phytanoyl-CoA hydroxylase (PHYH) and the PTS2 receptor (PEX7). Hum. Mutat. 23: 209-218, 2004. [PubMed: 14974078] [Full Text: https://doi.org/10.1002/humu.10315]
McDonough, M. A., Kavanagh, K. L., Butler, D., Searls, T., Oppermann, U., Schofield, C. J. Structure of human phytanoyl-CoA 2-hydroxylase identifies molecular mechanisms of Refsum disease. J. Biol. Chem. 280: 41101-41110, 2005. [PubMed: 16186124] [Full Text: https://doi.org/10.1074/jbc.M507528200]
Mihalik, S. J., Morrell, J. C., Kim. D., Sacksteder, K. A., Watkins, P. A., Gould, S. J. Identification of PAHX, a Refsum disease gene. Nature Genet. 17: 185-189, 1997. [PubMed: 9326939] [Full Text: https://doi.org/10.1038/ng1097-185]
Mihalik, S. J., Rainville, A. M., Watkins, P. A. Phytanic acid alpha-oxidation in rat liver peroxisomes: production of alpha-hydroxyphytanoyl-CoA and formate is enhanced by dioxygenase cofactors. Europ. J. Biochem. 232: 545-551, 1995. [PubMed: 7556205] [Full Text: https://doi.org/10.1111/j.1432-1033.1995.545zz.x]
Mukherji, M., Chien, W., Kershaw, N. J., Clifton, I. J., Schofield, C. J., Wierzbicki, A. S., Lloyd, M. D. Structure-function analysis of phytanoyl-CoA 2-hydroxylase mutations causing Refsum's disease. Hum. Molec. Genet. 10: 1971-1982, 2001. [PubMed: 11555634] [Full Text: https://doi.org/10.1093/hmg/10.18.1971]
Skjeldal, O. H., Stokke, O., Refsum, S., Norseth, J., Petit, H. Clinical and biochemical heterogeneity in conditions with phytanic acid accumulation. J. Neurol. Sci. 77: 87-96, 1987. [PubMed: 2433405] [Full Text: https://doi.org/10.1016/0022-510x(87)90209-7]
Watkins, P. A., Howard, A. E., Mihalik, S. J. Phytanic acid must be activated to phytanoyl-CoA prior to its alpha-oxidation in rat liver peroxisomes. Biochim. Biophys. Acta 1214: 288-294, 1994. [PubMed: 7918611] [Full Text: https://doi.org/10.1016/0005-2760(94)90075-2]