GENE REFERENCE / HGNC:4839

HCFC1

host cell factor C1

protein-coding geneXq28Gene information

What does this gene do?

The HCFC1 gene provides instructions for making a protein, called HCF-1, that helps regulate the activity of other genes. HCF-1 interacts with proteins called transcription factors, which attach (bind) to specific regions of DNA and help control the activity of particular genes.

One of several functions of the HCF-1 protein is to control the activity of a gene called MMACHC that is involved in the processing of vitamin B12 (also known as cobalamin). This gene plays a role in the conversion of vitamin B12 into one of two molecules, adenosylcobalamin (AdoCbl) or methylcobalamin (MeCbl). AdoCbl is required for the normal function of an enzyme known as methylmalonyl CoA mutase. This enzyme helps break down certain protein building blocks (amino acids), fat building blocks (fatty acids), and cholesterol. AdoCbl is called a cofactor because it helps methylmalonyl CoA mutase carry out its function. MeCbl is also a cofactor, but for an enzyme known as methionine synthase. This enzyme converts the amino acid homocysteine to another amino acid, methionine. The body uses methionine to make proteins and other important compounds.

HCF-1 helps regulate genes that are important in other cellular processes, such as progression of cells through the step-by-step process it takes to replicate themselves (called the cell cycle). This protein also plays a role in the distribution of cells in developing tissues and organs, including the brain.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-04-11. Source review: 2022-08.

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
X-linked intellectual disabilityMONDO:0100284 · Evaluated 2021-03-17	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: 2,040
Submissions for variants in or overlapping this gene: 2,804
Submissions explicitly reporting this gene: 2,471
Alleles reported pathogenic / likely pathogenic: 16
VariationIDs with uncertain significance: 430
VariationIDs with conflicting classifications: 63

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 HCFC1?

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 16 alleles in HCFC1 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 HCFC1.

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

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