SLC15A5

solute carrier family 15 member 5, the group of Solute carrier family 15

Basic information

Region (hg38): 12:16188485-16277685

Links

ENSG00000188991 ∙ NCBI:729025 ∙ ∙ HGNC:33455 ∙ Uniprot:A6NIM6 ∙ 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 SLC15A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC15A5 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			53	2		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	2	0

Variants in SLC15A5

This is a list of pathogenic ClinVar variants found in the SLC15A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-16189714-A-C		not specified	Uncertain significance (Aug 12, 2021)
12-16189733-G-C		not specified	Uncertain significance (May 22, 2023)
12-16189742-C-T		not specified	Uncertain significance (Mar 07, 2025)
12-16194408-A-C		not specified	Uncertain significance (Oct 26, 2021)
12-16194427-T-C		not specified	Uncertain significance (May 27, 2022)
12-16216919-A-T		not specified	Uncertain significance (Aug 17, 2022)
12-16216974-T-C		not specified	Uncertain significance (Jan 24, 2024)
12-16216997-G-T		not specified	Uncertain significance (Feb 14, 2023)
12-16217004-A-G		not specified	Uncertain significance (Sep 30, 2024)
12-16224507-C-T		not specified	Uncertain significance (Oct 04, 2024)
12-16224522-C-T		not specified	Uncertain significance (May 06, 2024)
12-16224577-C-A		not specified	Uncertain significance (Jan 18, 2022)
12-16239726-G-C		not specified	Uncertain significance (Mar 23, 2022)
12-16239746-A-G		not specified	Uncertain significance (Dec 16, 2023)
12-16239791-A-G		not specified	Uncertain significance (Nov 04, 2023)
12-16239829-G-T		not specified	Uncertain significance (Aug 05, 2024)
12-16239858-C-G		not specified	Uncertain significance (Feb 06, 2024)
12-16244638-A-G		not specified	Uncertain significance (Jan 04, 2022)
12-16244669-T-C		not specified	Uncertain significance (Sep 24, 2024)
12-16244689-T-C		not specified	Uncertain significance (Jan 08, 2024)
12-16244713-G-C		not specified	Uncertain significance (Jun 21, 2023)
12-16244747-G-A		not specified	Uncertain significance (Apr 27, 2022)
12-16244774-C-A		not specified	Uncertain significance (Dec 27, 2023)
12-16244777-C-T		not specified	Uncertain significance (Oct 11, 2024)
12-16244779-A-G		not specified	Uncertain significance (Nov 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC15A5	protein_coding	protein_coding	ENST00000344941	9	89201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-9	0.391	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.908	226	268	0.844	0.0000126	3734
Missense in Polyphen		49	60.158	0.81453		885
Synonymous	0.869	94	105	0.892	0.00000535	1138
Loss of Function	0.936	16	20.6	0.777	0.00000100	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton oligopeptide cotransporter. {ECO:0000305}.

Intolerance Scores

• rvis_EVS: 2.51
• rvis_percentile_EVS: 98.66

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc15a5

Gene ontology

• Biological process: protein transport;oligopeptide transmembrane transport;proton transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: protein binding;peptide:proton symporter activity;oligopeptide transmembrane transporter activity;peptide transmembrane transporter activity