SLC15A4

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

Basic information

Region (hg38): 12:128793194-128823958

Links

ENSG00000139370 ∙ NCBI:121260 ∙ OMIM:615806 ∙ HGNC:23090 ∙ Uniprot:Q8N697 ∙ 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 SLC15A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC15A4 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in SLC15A4

This is a list of pathogenic ClinVar variants found in the SLC15A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-128794203-C-T		not specified	Uncertain significance (Aug 30, 2022)
12-128794221-C-T		not specified	Uncertain significance (Jun 17, 2024)
12-128794224-T-C		not specified	Uncertain significance (Oct 12, 2021)
12-128794236-C-G		not specified	Uncertain significance (Mar 04, 2024)
12-128794238-C-G		not specified	Uncertain significance (Aug 03, 2022)
12-128794304-A-C		not specified	Uncertain significance (Jul 27, 2024)
12-128794306-T-C		not specified	Uncertain significance (Sep 08, 2024)
12-128794308-G-A		not specified	Uncertain significance (Jun 27, 2022)
12-128799328-C-A		not specified	Uncertain significance (Apr 08, 2023)
12-128799328-C-T		not specified	Uncertain significance (Jun 10, 2024)
12-128799368-T-C		not specified	Uncertain significance (Jul 02, 2024)
12-128799382-T-C		not specified	Uncertain significance (Oct 05, 2023)
12-128799411-T-C		not specified	Uncertain significance (Nov 09, 2021)
12-128799415-G-T		not specified	Uncertain significance (Feb 28, 2024)
12-128800883-C-T		not specified	Uncertain significance (May 17, 2023)
12-128800926-C-T		not specified	Uncertain significance (Jul 20, 2022)
12-128808875-T-C		not specified	Likely benign (Sep 01, 2021)
12-128808922-A-G		not specified	Uncertain significance (Jun 25, 2024)
12-128809992-A-G		not specified	Uncertain significance (Sep 04, 2024)
12-128809993-T-C		not specified	Uncertain significance (Feb 13, 2024)
12-128810011-C-T		not specified	Uncertain significance (Apr 13, 2023)
12-128814850-G-A		not specified	Uncertain significance (Oct 01, 2024)
12-128814881-C-A		not specified	Likely benign (Dec 19, 2022)
12-128814881-C-T		not specified	Uncertain significance (Mar 03, 2022)
12-128814938-C-A		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC15A4	protein_coding	protein_coding	ENST00000266771	8	30790

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000193	0.891	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	231	278	0.830	0.0000150	3643
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton oligopeptide cotransporter. Transports free histidine and certain di- and tripeptides. {ECO:0000269|PubMed:16289537}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System;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: 0.0941

Haploinsufficiency Scores

• pHI: 0.0594
• hipred: N
• hipred_score: 0.379
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.593

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc15a4
• Phenotype: immune system phenotype

Gene ontology

• Biological process: ion transport;protein transport;histidine transport;oligopeptide transmembrane transport;neutrophil degranulation;L-histidine transmembrane transport;proton transmembrane transport
• Cellular component: lysosomal membrane;plasma membrane;integral component of membrane;specific granule membrane
• Molecular function: L-histidine transmembrane transporter activity;protein binding;peptide:proton symporter activity;oligopeptide transmembrane transporter activity;peptide transmembrane transporter activity