Skip to content
Use your HSA or FSA funds
Sequence your genome (opens in a new tab)

Gene

PHYH

phytanoyl-CoA 2-hydroxylase

Summary

Cytogenetic location
10p13
Coordinates
Chromosome 10: 13,277,799–13,300,064 (GRCh38)
Exons
9 exons across 22.3 kb
Protein
338 amino acids
Also known as
PAHX, RD, PHYH1
MANE Select transcript
ENST00000263038.9NM_006214.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Peroxisomal Enzyme Disorders & Refsum Disease

    • Adult Refsum DiseaseAutosomal recessive

      Caused by variants in PHYH or PEX7, which lead to a build-up of phytanic acid and cause night blindness and retinitis pigmentosa, loss of smell, nerve damage and sometimes heart rhythm problems.

      • 5 GenCC submitters rate it definitive or strong
      Actionability

      Knowing allows a diet low in phytanic acid, which can halt progression of nerve and eye damage.

How PHYH is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 10, with a bracket where PHYH sits. PHYH and 9 genes near it on chromosome 10, from 12,788,932 to 13,788,931.Chromosome 1010p13p15.3p15.2p15.1p14p13p12.33p12.32p12.31p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.31q23.32q23.33q24.1q24.2q24.31q24.32q24.33q25.1q25.2q25.3q26.11q26.12q26.13q26.2q26.312.8 Mb13 Mb13.2 Mb13.4 Mb13.6 MbCAMK1D: 12,349,513–12,835,545, forward strandCAMK1DCCDC3: 12,896,625–13,099,652, reverse strandCCDC3OPTN: 13,099,442–13,159,480, forward strandOPTNMCM10: 13,161,526–13,211,110, forward strandMCM10UCMA: 13,220,609–13,234,428, reverse strandUCMAPHYH: 13,277,799–13,300,064, reverse strandPHYHSEPHS1: 13,317,425–13,348,596, reverse strandSEPHS1BEND7: 13,438,484–13,529,287, reverse strandBEND7PRPF18: 13,586,922–13,668,445, forward strandPRPF18FRMD4A: 13,643,706–14,462,142, reverse strandFRMD4ADiagram of PHYH: 9 exons on the reverse strand of chromosome 10Exon 8: 3 known disease-causing sitesExon 7: 10 known disease-causing sitesExon 6: 21 known disease-causing sitesExon 5: 4 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 3: 1 known disease-causing siteExon 2: 3 known disease-causing sitesExon 1: 3 known disease-causing sitesExon 9: 13,277,799–13,278,354, 556 basesExon 8: 13,280,976–13,281,110, 135 basesExon 7: 13,283,690–13,283,839, 150 basesExon 6: 13,288,360–13,288,541, 182 basesExon 5: 13,291,831–13,291,912, 82 basesExon 4: 13,294,428–13,294,596, 169 basesExon 3: 13,295,496–13,295,606, 111 basesExon 2: 13,298,187–13,298,245, 59 basesExon 1: 13,299,968–13,300,064, 97 bases9876543215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.5 kb of the gene's 22.3 kb; 1,017 of those bases code for the protein.

Sequencing PHYH

1Low

How hard PHYH is to sequence with short reads, out of 100

  • Mappability0%
  • Homology0%
  • Repeats2.4%
  • GC content6.3%
  • Reference coverage0%

60

positions in PHYH where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 22.3 kb of PHYH, introns included, not only the 1.5 kb of exons.

Traits linked to PHYH

The Human Phenotype Ontology lists these as features of the rare conditions PHYH can cause. Each trait's page lists the other genes linked to it.

External links

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-17: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.17-8666dff2.

Cite this page

APA

Dante Labs. (n.d.). PHYH gene: phytanoyl-CoA 2-hydroxylase. Retrieved 17 October 2026, from https://dantelabs.com/genes/phyh

Vancouver

Dante Labs. PHYH gene: phytanoyl-CoA 2-hydroxylase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/phyh

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test