SLC28A1

Chr 15AR

solute carrier family 28 member 1

Also known as: CNT1, HCNT1, URCTU

NCBI Gene: 9154 ENSG00000156222 UniProt: O00337 OMIM: 606207

The SLC28A1 protein is a sodium-coupled transporter that imports pyrimidine nucleosides (uridine, thymidine, cytidine) and adenosine into cells, particularly functioning in renal nucleoside reabsorption. Mutations cause uridine-cytidineuria, an autosomal recessive disorder. The gene shows low constraint against loss-of-function variants (high LOEUF score), consistent with a recessive inheritance pattern where heterozygous carriers are typically unaffected.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

Enables azole transmembrane transporter activity; pyrimidine- and adenosine-specific:sodium symporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport and nucleoside transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

[Uridine-cytidineuria]MIM #618477

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.25

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.25LOEUF

pLI 0.000

Z-score 0.39

OE 0.93 (0.70–1.25)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.74Z-score

OE missense 1.11 (1.02–1.21)

393 obs / 353.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.93 (0.70–1.25)

0≤0.351.4

Missense OE?1.11 (1.02–1.21)

0≤0.61.4

Synonymous OE?1.17

0≤1.21.6

LoF obs/exp: 31 / 33.4Missense obs/exp: 393 / 353.7Syn Z: -1.65

Background carrier burden — how many people carry a rare variant somewhere in SLC28A1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 47

918 rare PASS variants

Rare truncating (LoF)

1 in 430

146 rare PASS variants

Rare synonymous (reference)

1 in 100

396 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC28A1. 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 60	1 in 930
South Asian	~43k	1 in 46	1 in 670
Remaining (unassigned)	~30k	1 in 35	1 in 750
European (Finnish)	~27k	1 in 160	1 in 700
Admixed American	~22k	1 in 52	1 in 320
African / African American	~21k	1 in 46	1 in 220
East Asian	~20k	1 in 50	1 in 950
Ashkenazi Jewish	~13k	1 in 430	1 in 480
Middle Eastern	~2,884	1 in 44	1 in 550

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 17 coding exons well covered in gnomAD exomes and genomes.? see exons ↓