SLC15A2

protein-coding

solute carrier family 15 member 2, the group of Solute carrier family 15

Gene summary

The mammalian kidney expresses a proton-coupled peptide transporter that is responsible for the absorption of small peptides, as well as beta-lactam antibiotics and other peptide-like drugs, from the tubular filtrate. This transporter, SLC15A2, belongs to the same gene family as SLC15A1 (MIM 600544), the proton-coupled peptide transporter found in the small intestine (Liu et al, 1995 [PubMed 7756356]).[supplied by OMIM, Feb 2011]

MANE transcript

NM_021082.4

Inheritance

—

ClinVar variants

U:103B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr3:121,894,401-121,944,188

External References & Databases

Ensembl (ENSG00000163406)

Transcript & Mutation Effects

hg38 • Region Span ~49.8 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 SLC15A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 97

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021082.4. 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				1 clinvar	1 clinvar	2
missense			97 clinvar	4 clinvar		101
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	103	5	1	109

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021082.4	RefSeq	NP_066568.3	22	MANE Select
ENST00000489711.6	Ensembl	ENSP00000417085.1	22	MANE Select
NM_001145998.2	RefSeq	NP_001139470.1	21	Standard
ENST00000295605.6	Ensembl	ENSP00000295605.2	21	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
drug transport
dipeptide transmembrane transport
proton transmembrane transport

Molecular Function

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

Cellular Component

plasma membrane
integral component of plasma membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000489711
Coding exons: 22
Length: 50014
Individuals with no LoFs: 125641
Homozygous LoFs: 0
Heterozygous LoFs: 107
Defined: 125748
p: 0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.201	376	387	0.971	0.0000190	4784
Missense (PolyPhen)		86	100.44	0.8562		1200
Synonymous	0.00197	139	139	1.00	0.00000687	1408
Loss of Function	1.27	35	44.1	0.794	0.00000230	500

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00071	0.00071	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00037	0.00037	rare
South Asian	0.00059	0.00059	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Proton-coupled intake of oligopeptides of 2 to 4 amino acids with a preference for dipeptides (PubMed:7756356). Transports the dipeptide-like aminopeptidase inhibitor bestatin (By similarity). Can also transport the aminocephalosporin antibiotic cefadroxil (By similarity). {ECO:0000250|UniProtKB:P46029, ECO:0000250|UniProtKB:Q63424, ECO:0000269|PubMed:7756356}.;

Recessive Scores

pRec: 0.171

Intolerance Scores

LoFtool: 0.979
RVIS EVS: -0.18
RVIS percentile EVS: 40.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.146

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High