GENE REFERENCE / HGNC:8940

PHYH

phytanoyl-CoA 2-hydroxylase

protein-coding gene10p13Gene information

What does this gene do?

The PHYH gene provides instructions for making an enzyme called phytanoyl-CoA hydroxylase. This enzyme is critical for the normal function of cell structures called peroxisomes. These sac-like compartments contain enzymes needed to break down many different substances, including fatty acids and certain toxic compounds.

One substance that is broken down in peroxisomes is phytanic acid, a type of fatty acid obtained from the diet (particularly from beef and dairy products). Phytanoyl-CoA hydroxylase is responsible for one of the first steps in breaking down phytanic acid as part of a process known as alpha-oxidation. In subsequent steps, additional enzymes in peroxisomes and other parts of the cell further process this compound into smaller molecules that the body can use for energy.

Researchers suspect that phytanoyl-CoA hydroxylase may have other functions in addition to its role in breaking down phytanic acid. For example, this enzyme appears to help determine the number of peroxisomes within cells and is involved in regulating their activity.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2010-01.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
phytanoyl-CoA hydroxylase deficiencyMONDO:0100258 · Evaluated 2020-02-07	Autosomal recessive	DefinitivePeroxisomal Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 593
Submissions for variants in or overlapping this gene: 1,045
Submissions explicitly reporting this gene: 991
Alleles reported pathogenic / likely pathogenic: 114
VariationIDs with uncertain significance: 201
VariationIDs with conflicting classifications: 24

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about PHYH?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 114 alleles in PHYH reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in PHYH.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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