SLC28A2

Chr 15

solute carrier family 28 member 2

Also known as: CNT2, HCNT2, HsT17153, SPNT1

NCBI Gene: 9153 ENSG00000137860 UniProt: O43868 OMIM: 606208

Enables neurotransmitter transmembrane transporter activity and nucleoside transmembrane transporter activity. Involved in neurotransmitter transport; nucleoside transport; and purine nucleobase transmembrane transport. Located in apicolateral plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.53

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.53LOEUF

pLI 0.000

Z-score -0.89

OE 1.17 (0.90–1.53)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.09Z-score

OE missense 0.99 (0.90–1.08)

349 obs / 353.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.17 (0.90–1.53)

0≤0.351.4

Missense OE?0.99 (0.90–1.08)

0≤0.61.4

Synonymous OE?0.99

0≤1.21.6

LoF obs/exp: 38 / 32.5Missense obs/exp: 349 / 353.8Syn Z: 0.05

Background carrier burden — how many people carry a rare variant somewhere in SLC28A2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 82

814 rare PASS variants

Rare truncating (LoF)

1 in 340

163 rare PASS variants

Rare synonymous (reference)

1 in 160

321 rare PASS variants

Rare missense and truncating variants are carried at similar rates in SLC28A2; this gene does not show strong loss-of-function constraint by this measure. 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 110	1 in 340
South Asian	~43k	1 in 55	1 in 530
Remaining (unassigned)	~30k	1 in 83	1 in 300
European (Finnish)	~27k	1 in 170	1 in 640
Admixed American	~22k	1 in 76	1 in 590
African / African American	~21k	1 in 58	1 in 680
East Asian	~20k	1 in 110	1 in 560
Ashkenazi Jewish	~13k	1 in 180	none seen
Middle Eastern	~2,884	1 in 80	1 in 360

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): 15 of 17 coding exons well covered in gnomAD exomes; exons 17, 18 marginal. Genomes: all 17.? see exons ↓