GENE REFERENCE / HGNC:23096

SLC29A3

solute carrier family 29 member 3

protein-coding gene10q22.1Gene information

What does this gene do?

The SLC29A3 gene provides instructions for making a protein called equilibrative nucleoside transporter 3 (ENT3). ENT3 belongs to a family of proteins that transport molecules called nucleosides in cells. With chemical modification, nucleosides become the building blocks of DNA, its chemical cousin RNA, and molecules such as ATP and GTP, which serve as energy sources in the cell. Molecules derived from nucleosides play an important role in many functions throughout the body.

ENT3 is found in the membranes surrounding cell structures known as lysosomes and mitochondria. Lysosomes are compartments within the cell that use digestive enzymes to break down large molecules into smaller ones that can be reused by cells. Researchers believe that ENT3 transports nucleosides generated by the breakdown of DNA and RNA out of lysosomes into the cell so they can be reused.

Mitochondria are structures within cells that convert the energy from food into a form that cells can use. While most DNA is packaged in chromosomes within the nucleus, mitochondria also have a small amount of their own DNA (called mitochondrial DNA). Researchers believe that the ENT3 protein in mitochondrial membranes helps transport nucleosides into mitochondria; the nucleosides can then be used for the formation or repair of mitochondrial DNA and RNA, which are essential for proper functioning of the structures.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2014-12.

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
H syndromeMONDO:0011273 · Evaluated 2024-05-07	Autosomal recessive	DefinitiveLysosomal Diseases 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: 607
Submissions for variants in or overlapping this gene: 1,063
Submissions explicitly reporting this gene: 1,033
Alleles reported pathogenic / likely pathogenic: 53
VariationIDs with uncertain significance: 257
VariationIDs with conflicting classifications: 31

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 SLC29A3?

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 53 alleles in SLC29A3 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 SLC29A3.

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

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