GENE REFERENCE / HGNC:3663

FGD1

FYVE, RhoGEF and PH domain containing 1

protein-coding geneXp11.22Gene information

What does this gene do?

The FGD1 gene provides instructions for making a protein that functions as a guanine nucleotide exchange factor (GEF). GEFs turn on (activate) proteins called GTPases, which play an important role in chemical signaling within cells. GTPases are turned off (inactivated) when they are attached (bound) to a molecule called GDP and are turned on (activated) when they are bound to another molecule called GTP.

The FGD1 protein activates the GTPase known as Cdc42 by stimulating the exchange of GDP for GTP. Once Cdc42 is active, it transmits signals that are critical for various aspects of development before and after birth, particularly the development of bones. The FGD1 protein may also be involved in maintenance (remodeling) of the extracellular matrix, which is the intricate lattice of proteins and other molecules that forms in the spaces between cells. Through this process, the protein appears to play a role in cell movement (migration) and the remodeling of blood vessels.

Source: MedlinePlus, National Library of Medicine. Source publication: 2022-05-27. Source review: 2022-06.

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
Aarskog-Scott syndrome, X-linkedMONDO:0010589 · Evaluated 2017-12-06	X-linked	DefinitiveIntellectual Disability and Autism 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: 774
Submissions for variants in or overlapping this gene: 1,139
Submissions explicitly reporting this gene: 964
Alleles reported pathogenic / likely pathogenic: 106
VariationIDs with uncertain significance: 239
VariationIDs with conflicting classifications: 37

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 FGD1?

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 106 alleles in FGD1 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 FGD1.

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

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