SLC29A2

Chr 11

solute carrier family 29 member 2

Also known as: DER12, ENT2, HNP36, hENT2

NCBI Gene: 3177 ENSG00000174669 UniProt: Q14542 OMIM: 602110

The SLC29A2 protein functions as a bidirectional transporter that facilitates the movement of nucleosides (such as adenosine, inosine, and uridine) and nucleobases across cell membranes, maintaining cellular nucleoside homeostasis essential for nucleotide synthesis. Mutations cause microcephaly, seizures, and developmental delay with autosomal recessive inheritance. The disorder affects the central nervous system primarily, with onset typically in early infancy.

OMIM ResearchSummary from RefSeq, UniProt

The uptake of nucleosides by transporters, such as SLC29A2, is essential for nucleotide synthesis by salvage pathways in cells that lack de novo biosynthetic pathways. Nucleoside transport also plays a key role in the regulation of many physiologic processes through its effect on adenosine concentration at the cell surface (Griffiths et al., 1997 [PubMed 9396714]).[supplied by OMIM, Nov 2008]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.41

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.41LOEUF

pLI 0.000

Z-score 0.08

OE 0.98 (0.69–1.41)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.48Z-score

OE missense 0.92 (0.82–1.02)

236 obs / 257.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.98 (0.69–1.41)

0≤0.351.4

Missense OE?0.92 (0.82–1.02)

0≤0.61.4

Synonymous OE?0.83

0≤1.21.6

LoF obs/exp: 21 / 21.4Missense obs/exp: 236 / 257.7Syn Z: 1.46

Background carrier burden — how many people carry a rare variant somewhere in SLC29A2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 83

609 rare PASS variants

Rare truncating (LoF)

1 in 700

91 rare PASS variants

Rare synonymous (reference)

1 in 160

201 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC29A2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 120	1 in 620
South Asian	~43k	1 in 66	1 in 860
Remaining (unassigned)	~30k	1 in 78	1 in 860
European (Finnish)	~27k	1 in 360	≈ 1 in 8,900
Admixed American	~22k	1 in 77	1 in 1,800
African / African American	~21k	1 in 58	1 in 1,200
East Asian	~20k	1 in 64	1 in 960
Ashkenazi Jewish	~13k	1 in 190	≈ 1 in 4,300
Middle Eastern	~2,884	1 in 80	≈ 1 in 1,300

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 12 coding exons well covered in gnomAD exomes and genomes.? see exons ↓