SLC36A4

Chr 11

solute carrier family 36 member 4

Also known as: PAT4

NCBI Gene: 120103 ENSG00000180773 UniProt: Q6YBV0 OMIM: 613760

SLC36A4 belongs to the SLC36 family of amino acid transporters based on sequence similarity with other family members (e.g., SLC36A1; MIM 606561). SLC36 proteins contain about 500 amino acids and have 9 to 11 transmembrane domains. Unlike other SLC36 family members, which are proton-coupled amino acid transporters, SLC36A4 is a high-affinity/low-capacity non-proton-coupled amino acid transporter (Pillai and Meredith, 2011 [PubMed 21097500]).[supplied by OMIM, Feb 2011]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.59

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.59LOEUF

pLI 0.000

Z-score -0.57

OE 1.13 (0.82–1.59)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.04Z-score

OE missense 1.01 (0.91–1.12)

261 obs / 259.1 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.13 (0.82–1.59)

0≤0.351.4

Missense OE?1.01 (0.91–1.12)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 24 / 21.2Missense obs/exp: 261 / 259.1Syn Z: 0.50

Background carrier burden — how many people carry a rare variant somewhere in SLC36A4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 77

648 rare PASS variants

Rare truncating (LoF)

1 in 710

126 rare PASS variants

Rare synonymous (reference)

1 in 110

230 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC36A4. 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 99	1 in 850
South Asian	~43k	1 in 71	1 in 810
Remaining (unassigned)	~30k	1 in 60	1 in 480
European (Finnish)	~27k	1 in 180	≈ 1 in 27,000
Admixed American	~22k	1 in 80	1 in 670
African / African American	~21k	1 in 82	1 in 730
East Asian	~20k	1 in 84	1 in 590
Ashkenazi Jewish	~13k	1 in 520	≈ 1 in 6,300
Middle Eastern	~2,881	1 in 75	1 in 470

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): 8 of 11 coding exons well covered in gnomAD exomes; exons 3, 5, 10 marginal. Genomes: all 11.? see exons ↓