GENE REFERENCE / HGNC:30521

SLC46A1

solute carrier family 46 member 1

protein-coding gene17q11.2Gene information

What does this gene do?

The SLC46A1 gene provides instructions for making a protein called the proton-coupled folate transporter (PCFT). This protein is found within the membrane of cells, where it helps transport certain B vitamins called folates into the cell. PCFT is primarily found in cells that line the walls of the small intestine. These cells have fingerlike projections called microvilli that absorb nutrients from food as it passes through the intestine. Based on their appearance, groups of these microvilli are known collectively as the brush border. PCFT is involved in transporting folates from food across the brush border membrane so they can be used by the body. PCFT is also found in the brain, where it is involved in the transport of folates between the brain and the surrounding fluid (cerebrospinal fluid).

Source: MedlinePlus, National Library of Medicine. Source publication: 2024-05-22. Source review: 2024-05.

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
hereditary folate malabsorptionMONDO:0009238 · Evaluated 2026-07-16	Autosomal recessive	DefinitiveSCID-CID 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: 439
Submissions for variants in or overlapping this gene: 625
Submissions explicitly reporting this gene: 601
Alleles reported pathogenic / likely pathogenic: 26
VariationIDs with uncertain significance: 218
VariationIDs with conflicting classifications: 19

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 SLC46A1?

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 26 alleles in SLC46A1 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 SLC46A1.

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

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