SLC22A15

protein-coding

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

Gene summary

Organic ion transporters, such as SLC22A15, transport various medically and physiologically important compounds, including pharmaceuticals, toxins, hormones, neurotransmitters, and cellular metabolites. These transporters are also referred to as amphiphilic solute facilitators (ASFs).[supplied by OMIM, Apr 2004]

MANE transcript

NM_018420.3

Inheritance

—

ClinVar variants

U:76B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr1:115,976,513-116,070,054

External References & Databases

Ensembl (ENSG00000163393)

Transcript & Mutation Effects

hg38 • Region Span ~93.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC22A15 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018420.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			73 clinvar	4 clinvar		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	4	0	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018420.3	RefSeq	NP_060890.2	12	MANE Select
ENST00000369503.9	Ensembl	ENSP00000358515.4	12	MANE Select
ENST00000369502.1	Ensembl	ENSP00000358514.1	6	Standard
ENST00000369502.2	Ensembl	ENSP00000358514.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

ion transport
transmembrane transport

Molecular Function

transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369503
Coding exons: 12
Length: 93557
Individuals with no LoFs: 124594
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 124658
p: 0.000257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.676	270	303	0.891	0.0000164	3500
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.00080	0.00080	rare
East Asian	0.00063	0.00061	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00032	0.00031	rare
South Asian	0.000099	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probably transports organic cations (By similarity). Appears not to be the agmatine transporter. {ECO:0000250, ECO:0000269|PubMed:15028572}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.808
RVIS EVS: 0.04
RVIS percentile EVS: 57.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.509

Gene Damage Prediction

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