SLC15A3

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

Basic information

Region (hg38): 11:60937060-60952653

Links

ENSG00000110446 ∙ NCBI:51296 ∙ OMIM:610408 ∙ HGNC:18068 ∙ Uniprot:Q8IY34 ∙ 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 SLC15A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC15A3 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						0
missense			34	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	2	0

Variants in SLC15A3

This is a list of pathogenic ClinVar variants found in the SLC15A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60937241-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-60937242-G-A		not specified	Likely benign (Dec 08, 2023)
11-60937281-G-A		not specified	Uncertain significance (Aug 07, 2024)
11-60937311-T-C		not specified	Uncertain significance (Nov 12, 2021)
11-60937355-C-T		not specified	Uncertain significance (Jun 16, 2024)
11-60937366-G-C		not specified	Uncertain significance (Jun 19, 2024)
11-60937900-C-A		not specified	Uncertain significance (Jun 29, 2022)
11-60937900-C-G		not specified	Uncertain significance (May 21, 2024)
11-60937900-C-T		not specified	Uncertain significance (Apr 17, 2023)
11-60937917-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-60937953-G-A		not specified	Uncertain significance (Sep 09, 2024)
11-60937989-A-C		not specified	Uncertain significance (Nov 24, 2024)
11-60937996-G-A		not specified	Uncertain significance (Oct 27, 2022)
11-60937998-G-A		not specified	Uncertain significance (Oct 12, 2024)
11-60938020-C-G		not specified	Uncertain significance (Nov 18, 2022)
11-60939524-T-C		not specified	Uncertain significance (Feb 28, 2023)
11-60939621-G-A		not specified	Uncertain significance (Oct 20, 2021)
11-60941131-T-A		not specified	Uncertain significance (Dec 20, 2023)
11-60941139-G-A		not specified	Uncertain significance (Jun 29, 2022)
11-60941163-G-A		not specified	Uncertain significance (Jan 29, 2024)
11-60941220-A-G		not specified	Uncertain significance (Mar 29, 2023)
11-60941224-G-A		not specified	Uncertain significance (Nov 09, 2023)
11-60941256-A-G		not specified	Uncertain significance (Jun 16, 2023)
11-60941260-C-G		not specified	Uncertain significance (Jan 18, 2023)
11-60942057-C-G		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC15A3	protein_coding	protein_coding	ENST00000227880	8	15447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.78e-12	0.0726	125558	0	190	125748	0.000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	244	301	0.811	0.0000179	3638
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00419	0.00412
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.00115	0.00114
Finnish	0.0000966	0.0000924
European (Non-Finnish)	0.000420	0.000387
Middle Eastern	0.00115	0.00114
South Asian	0.00147	0.00144
Other	0.000515	0.000489

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0944

Haploinsufficiency Scores

• pHI: 0.216
• hipred: N
• hipred_score: 0.170
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.547

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc15a3
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype; immune system phenotype

Gene ontology

• Biological process: ion transport;protein transport;oligopeptide transmembrane transport;proton transmembrane transport
• Cellular component: lysosomal membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;peptide:proton symporter activity;oligopeptide transmembrane transporter activity;peptide transmembrane transporter activity