SLC15A4

protein-coding

solute carrier family 15 member 4, the group of Solute carrier family 15

Gene summary

Enables transmembrane transporter activity. Involved in dipeptide import across plasma membrane; peptidoglycan transport; and positive regulation of pattern recognition receptor signaling pathway. Located in endolysosome membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_145648.4

Inheritance

—

ClinVar variants

U:80B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr12:128,793,194-128,823,958

External References & Databases

Ensembl (ENSG00000139370)

Transcript & Mutation Effects

hg38 • Region Span ~30.8 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 SLC15A4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145648.4. 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			4 clinvar	1 clinvar		5
missense			74 clinvar	4 clinvar		78
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	80	5	0	85

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145648.4	RefSeq	NP_663623.1	8	MANE Select
ENST00000266771.10	Ensembl	ENSP00000266771.5	8	MANE Select
ENST00000376740.8	Ensembl	ENSP00000365930.5	3	Standard
ENST00000376744.8	Ensembl	ENSP00000365935.4	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Innate Immune System
Immune System
Proton/oligopeptide cotransporters
Amino acid and oligopeptide SLC transporters

Biological Process

ion transport
protein transport
histidine transport
oligopeptide transmembrane transport
neutrophil degranulation

Molecular Function

L-histidine transmembrane transporter activity
protein binding
peptide:proton symporter activity
oligopeptide transmembrane transporter activity
peptide transmembrane transporter activity

Cellular Component

lysosomal membrane
plasma membrane
integral component of membrane
specific granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266771
Coding exons: 8
Length: 30790
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125748
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	231	278	0.830	0.0000150	3643
Missense (PolyPhen)		59	81.015	0.72826		1076
Synonymous	-0.305	124	120	1.04	0.00000755	1228
Loss of Function	1.59	12	19.6	0.613	9.82e-7	226

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Proton oligopeptide cotransporter. Transports free histidine and certain di- and tripeptides. {ECO:0000269|PubMed:16289537}.;

Recessive Scores

pRec: 0.0941

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.593

Gene Damage Prediction

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