SLC15A1

solute carrier family 15 member 1, the group of Solute carrier family 15

Basic information

Region (hg38): 13:98683800-98752672

Links

ENSG00000088386 ∙ NCBI:6564 ∙ OMIM:600544 ∙ HGNC:10920 ∙ Uniprot:P46059 ∙ 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 SLC15A1 gene.

• Inborn genetic diseases (26 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC15A1 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					3	3
missense			24	2	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	24	2	5

Variants in SLC15A1

This is a list of pathogenic ClinVar variants found in the SLC15A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-98684848-C-T		not specified	Uncertain significance (Jul 15, 2021)
13-98684851-G-C		not specified	Uncertain significance (May 25, 2022)
13-98684886-C-G		not specified	Uncertain significance (Nov 15, 2021)
13-98686269-T-C		not specified	Uncertain significance (Jan 10, 2022)
13-98686278-G-A		not specified	Uncertain significance (Aug 17, 2021)
13-98686283-C-T		not specified	Uncertain significance (Dec 05, 2022)
13-98687583-G-C		not specified	Uncertain significance (Feb 15, 2023)
13-98687667-T-C		not specified	Uncertain significance (Jan 30, 2024)
13-98688316-A-G		not specified	Uncertain significance (Dec 21, 2023)
13-98688349-A-G		not specified	Uncertain significance (Apr 08, 2022)
13-98688471-T-C		not specified	Likely benign (Jan 06, 2023)
13-98688473-C-T		not specified	Uncertain significance (Aug 14, 2023)
13-98688539-A-G		not specified	Uncertain significance (Apr 22, 2022)
13-98702500-T-C			Benign (Jul 17, 2018)
13-98704306-G-A		not specified	Uncertain significance (Jun 21, 2023)
13-98704326-T-A		not specified	Uncertain significance (Dec 27, 2023)
13-98704419-G-A		not specified	Uncertain significance (Dec 21, 2022)
13-98706224-G-A			Benign (Jul 17, 2018)
13-98706263-A-G			Benign (May 24, 2018)
13-98708703-C-T		not specified	Uncertain significance (Nov 06, 2023)
13-98708754-T-C		not specified	Uncertain significance (May 31, 2023)
13-98709639-C-T		not specified	Uncertain significance (Jan 25, 2023)
13-98709889-G-C		not specified	Uncertain significance (Dec 18, 2023)
13-98711912-G-A		not specified	Likely benign (Dec 01, 2022)
13-98711939-C-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC15A1	protein_coding	protein_coding	ENST00000376503	23	68854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.99e-13	0.933	125636	0	112	125748	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0404	401	399	1.01	0.0000212	4682
Missense in Polyphen		91	95.895	0.94895		1143
Synonymous	0.634	145	155	0.935	0.00000976	1328
Loss of Function	2.13	26	40.6	0.640	0.00000203	462

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000711	0.000710
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00202	0.00201
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000308	0.000308
Middle Eastern	0.00202	0.00201
South Asian	0.000361	0.000359
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton-coupled intake of oligopeptides of 2 to 4 amino acids with a preference for dipeptides. May constitute a major route for the absorption of protein digestion end-products.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Statin Pathway - Generalized, Pharmacokinetics;Fluvastatin Pathway, Pharmacokinetics;Ibuprofen Pathway, Pharmacokinetics;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: 0.196

Intolerance Scores

• loftool: 0.883
• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.81

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.649
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc15a1
• Phenotype: digestive/alimentary phenotype

Gene ontology

• Biological process: ion transport;protein transport;dipeptide transmembrane transport;proton transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;brush border;integral component of membrane
• Molecular function: proton-dependent oligopeptide secondary active transmembrane transporter activity;peptide:proton symporter activity;oligopeptide transmembrane transporter activity;dipeptide transmembrane transporter activity;peptide transmembrane transporter activity