SLC15A2

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

Basic information

Region (hg38): 3:121894401-121944188

Links

ENSG00000163406 ∙ NCBI:6565 ∙ OMIM:602339 ∙ HGNC:10921 ∙ Uniprot:Q16348 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC15A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC15A2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			48	2		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	3	1

Variants in SLC15A2

This is a list of pathogenic ClinVar variants found in the SLC15A2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-121894490-A-G		not specified	Uncertain significance (Sep 21, 2023)
3-121894492-A-C		not specified	Uncertain significance (Mar 03, 2025)
3-121894514-T-C		not specified	Uncertain significance (Nov 24, 2024)
3-121894547-C-T		not specified	Uncertain significance (Sep 26, 2024)
3-121894580-C-T		not specified	Uncertain significance (Aug 27, 2024)
3-121896409-A-G		not specified	Uncertain significance (Feb 04, 2025)
3-121896412-T-C		not specified	Uncertain significance (May 10, 2022)
3-121896425-A-G		not specified	Uncertain significance (Jan 19, 2024)
3-121896437-T-C		not specified	Uncertain significance (Oct 03, 2022)
3-121896440-C-G		not specified	Uncertain significance (Jan 23, 2023)
3-121896488-T-C		not specified	Uncertain significance (Nov 25, 2024)
3-121897414-T-A		not specified	Uncertain significance (Jun 21, 2023)
3-121897511-C-T		not specified	Uncertain significance (Aug 12, 2021)
3-121911600-A-G		not specified	Uncertain significance (Jan 08, 2024)
3-121913037-G-A		not specified	Uncertain significance (Nov 15, 2024)
3-121913038-G-A		not specified	Uncertain significance (Jan 02, 2025)
3-121913117-A-C		not specified	Uncertain significance (Nov 07, 2024)
3-121915643-G-T		not specified	Uncertain significance (Oct 25, 2024)
3-121915657-T-C		not specified	Uncertain significance (Jun 07, 2023)
3-121915670-G-T		not specified	Uncertain significance (Feb 07, 2023)
3-121915682-T-C		not specified	Uncertain significance (Aug 20, 2024)
3-121922295-G-A		not specified	Uncertain significance (Apr 07, 2022)
3-121922777-T-A		not specified	Uncertain significance (Nov 17, 2022)
3-121923070-A-C		not specified	Uncertain significance (Nov 13, 2023)
3-121923223-G-A		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC15A2	protein_coding	protein_coding	ENST00000489711	22	50014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.48e-20	0.0790	125641	0	107	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.201	376	387	0.971	0.0000190	4784
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00146	0.00146
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000707	0.000707
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000375	0.000369
Middle Eastern	0.000707	0.000707
South Asian	0.000594	0.000588
Other	0.000491	0.000489

dbNSFP

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}.
• Pathway: 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;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.979
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.56

Haploinsufficiency Scores

• pHI: 0.613
• hipred: N
• hipred_score: 0.322
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.146

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc15a2
• Phenotype: renal/urinary system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: ion transport;protein transport;drug transport;dipeptide transmembrane transport;proton transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: protein binding;peptide:proton symporter activity;oligopeptide transmembrane transporter activity;dipeptide transmembrane transporter activity;peptide transmembrane transporter activity