SLC15A3

protein-coding

solute carrier family 15 member 3, the group of Solute carrier family 15

Gene summary

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

MANE transcript

NM_016582.3

Inheritance

—

ClinVar variants

U:102B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr11:60,937,060-60,952,653

External References & Databases

Ensembl (ENSG00000110446)

Transcript & Mutation Effects

hg38 • Region Span ~15.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC15A3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016582.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			99 clinvar	5 clinvar		104
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	102	6	0	108

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016582.3	RefSeq	NP_057666.1	8	MANE Select
ENST00000227880.8	Ensembl	ENSP00000227880.2	8	MANE Select
ENST00000536491.2	Ensembl	ENSP00000439535.2	7	Standard
ENST00000536784.6	Ensembl	ENSP00000441694.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Proton/oligopeptide cotransporters
Amino acid and oligopeptide SLC transporters
Transport of inorganic cations/anions and amino acids/oligopeptides
SLC-mediated transmembrane transport
Transport of small molecules

Biological Process

ion transport
protein transport
oligopeptide transmembrane transport
proton transmembrane transport

Molecular Function

protein binding
peptide:proton symporter activity
oligopeptide transmembrane transporter activity
peptide transmembrane transporter activity

Cellular Component

lysosomal membrane
integral component of membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000227880
Coding exons: 8
Length: 15447
Individuals with no LoFs: 125558
Homozygous LoFs: 0
Heterozygous LoFs: 190
Defined: 125748
p: 0.000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.17	244	301	0.811	0.0000179	3638
Missense (PolyPhen)		104	122.56	0.84853		1478
Synonymous	0.668	128	138	0.928	0.00000884	1273
Loss of Function	0.322	18	19.5	0.921	9.29e-7	222

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0037	0.0036	notable
Latino/Admixed American	0.00054	0.00049	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0011	0.0011	notable
Finnish	0.000097	0.000092	rare
European (Non-Finnish)	0.00042	0.00039	rare
South Asian	0.0015	0.0014	notable
Other	0.00052	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Proton oligopeptide cotransporter. Transports free histidine and certain di- and tripeptides (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0944

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.547

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium