GENE REFERENCE / HGNC:15465

GPHN

gephyrin

protein-coding gene14q23.3Gene information

What does this gene do?

The GPHN gene provides instructions for making a protein called gephyrin, which has two major functions in the body: the protein aids in the formation (biosynthesis) of a molecule called molybdenum cofactor, and it also plays a role in communication between nerve cells (neurons).

Gephyrin performs the final two steps in molybdenum cofactor biosynthesis. Molybdenum cofactor, which contains the element molybdenum, is essential to the function of several enzymes called sulfite oxidase, aldehyde oxidase, xanthine dehydrogenase, and mitochondrial amidoxime reducing component (mARC). These enzymes help break down (metabolize) different substances in the body, some of which are toxic if not metabolized.

Gephyrin also plays an important role in neurons. Communication between neurons depends on chemicals called neurotransmitters. To relay signals, a neuron releases neurotransmitters, which attach to receptor proteins on neighboring neurons. Gephyrin anchors certain receptor proteins to the correct location in neurons so that the receptors can receive the signals relayed by neurotransmitters.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2014-03.

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
sulfite oxidase deficiency due to molybdenum cofactor deficiency type CMONDO:0014212 · Evaluated 2023-05-12	Autosomal recessive	ModerateGeneral Inborn Errors of Metabolism 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: 2,680
Submissions for variants in or overlapping this gene: 3,891
Submissions explicitly reporting this gene: 1,159
Alleles reported pathogenic / likely pathogenic: 255
VariationIDs with uncertain significance: 1,379
VariationIDs with conflicting classifications: 12

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 GPHN?

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 255 alleles in GPHN 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 GPHN.

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

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