SLC22A15

solute carrier family 22 member 15, the group of Solute carrier family 22

Basic information

Region (hg38): 1:115976513-116070054

Links

ENSG00000163393 ∙ NCBI:55356 ∙ OMIM:608275 ∙ HGNC:20301 ∙ Uniprot:Q8IZD6 ∙ 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 SLC22A15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A15 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			39	3		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	3	0

Variants in SLC22A15

This is a list of pathogenic ClinVar variants found in the SLC22A15 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-115976653-C-A		not specified	Uncertain significance (Nov 21, 2023)
1-115976670-A-G		not specified	Uncertain significance (Jun 24, 2022)
1-115976674-A-C		not specified	Uncertain significance (Feb 21, 2024)
1-115976676-C-G		not specified	Uncertain significance (Sep 13, 2023)
1-115992077-C-G		not specified	Uncertain significance (May 26, 2023)
1-115992159-T-A		not specified	Likely benign (Aug 09, 2021)
1-115992166-T-G		not specified	Uncertain significance (Mar 28, 2022)
1-115992223-T-G		not specified	Uncertain significance (Oct 23, 2024)
1-115992235-G-A		not specified	Uncertain significance (Feb 24, 2025)
1-116019615-A-C		not specified	Uncertain significance (Jul 13, 2022)
1-116019685-G-A		not specified	Uncertain significance (Apr 23, 2024)
1-116020730-T-C		not specified	Uncertain significance (Nov 23, 2021)
1-116020753-A-G		not specified	Uncertain significance (Apr 25, 2023)
1-116020760-T-A		not specified	Uncertain significance (Mar 08, 2024)
1-116020769-C-T		not specified	Uncertain significance (Sep 20, 2024)
1-116020837-T-C		not specified	Uncertain significance (Apr 19, 2023)
1-116020847-T-C		not specified	Uncertain significance (Apr 25, 2023)
1-116020849-A-C		not specified	Uncertain significance (Apr 20, 2023)
1-116020861-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-116020867-G-T		not specified	Uncertain significance (Oct 25, 2022)
1-116020879-C-T		not specified	Uncertain significance (Mar 12, 2024)
1-116026958-C-T		not specified	Uncertain significance (May 23, 2023)
1-116026959-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-116031436-C-T		not specified	Uncertain significance (Aug 20, 2024)
1-116031454-C-T		not specified	Uncertain significance (Nov 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A15	protein_coding	protein_coding	ENST00000369503	12	93557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.52e-9	0.895	124594	0	64	124658	0.000257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.676	270	303	0.891	0.0000164	3500
Missense in Polyphen		93	121.9	0.76292		1393
Synonymous	1.32	107	126	0.850	0.00000714	1114
Loss of Function	1.79	18	28.3	0.637	0.00000143	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000803	0.000795
East Asian	0.000635	0.000612
Finnish	0.0000931	0.0000928
European (Non-Finnish)	0.000316	0.000310
Middle Eastern	0.000635	0.000612
South Asian	0.0000992	0.0000980
Other	0.000334	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably transports organic cations (By similarity). Appears not to be the agmatine transporter. {ECO:0000250, ECO:0000269|PubMed:15028572}.
• Pathway: Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Organic cation transport;Organic cation/anion/zwitterion transport (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.808
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.441
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.509

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a15

Gene ontology

• Biological process: ion transport;transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: transmembrane transporter activity