SLC15A3

Chr 11

solute carrier family 15 member 3

Also known as: OCTP, PHT2, PTR3, hPHT2

NCBI Gene: 51296 ENSG00000110446 UniProt: Q8IY34 OMIM: 610408

This proton-coupled transporter moves histidine, dipeptides, and tripeptides across membranes and plays a role in innate immune responses by transporting bacterial peptidoglycans like muramyl dipeptide. The gene shows no constraint against loss-of-function variants (pLI near zero, LOEUF >1), suggesting that complete loss of function may be tolerated. No established human disease associations have been reported for SLC15A3 mutations.

OMIM ResearchSummary from RefSeq, UniProt

Enables dipeptide transmembrane transporter activity. Involved in dipeptide import across plasma membrane. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.37

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.37LOEUF

pLI 0.000

Z-score 0.32

OE 0.92 (0.64–1.37)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.17Z-score

OE missense 0.81 (0.73–0.90)

244 obs / 301.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.92 (0.64–1.37)

0≤0.351.4

Missense OE?0.81 (0.73–0.90)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 18 / 19.5Missense obs/exp: 244 / 301.0Syn Z: 0.67

Background carrier burden — how many people carry a rare variant somewhere in SLC15A3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 42

892 rare PASS variants

Rare truncating (LoF)

1 in 350

134 rare PASS variants

Rare synonymous (reference)

1 in 100

333 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC15A3. 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 66	1 in 380
South Asian	~43k	1 in 47	1 in 210
Remaining (unassigned)	~30k	1 in 40	1 in 310
European (Finnish)	~27k	1 in 170	1 in 4,700
Admixed American	~22k	1 in 60	1 in 370
African / African American	~21k	1 in 55	1 in 590
East Asian	~20k	1 in 72	1 in 690
Ashkenazi Jewish	~13k	1 in 230	1 in 1,000
Middle Eastern	~2,884	1 in 55	1 in 400

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): 7 of 8 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 8.? see exons ↓