SLC22A13

protein-coding

solute carrier family 22 member 13, the group of Solute carrier family 22

Gene summary

This gene encodes a member of the organic-cation transporter family. It is located in a gene cluster with another member of the family, organic cation transporter like 4. The encoded protein is a transmembrane protein involved in the transport of small molecules. This protein can function to mediate urate uptake and is a high affinity nicotinate exchanger in the kidneys and the intestine. [provided by RefSeq, Sep 2008]

Previous symbols:

ORCTL3

MANE transcript

NM_004256.4

Inheritance

—

ClinVar variants

U:75B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.96

Max pathogenic AF

—

Genomic locus

chr3:38,265,812-38,278,757

External References & Databases

Ensembl (ENSG00000172940)

Transcript & Mutation Effects

hg38 • Region Span ~12.9 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 SLC22A13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004256.4. 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			74 clinvar	9 clinvar	1 clinvar	84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	75	11	1	87

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004256.4	RefSeq	NP_004247.2	10	MANE Select
ENST00000311856.9	Ensembl	ENSP00000310241.3	10	MANE Select
ENST00000415844.1	Ensembl	ENSP00000395106.1	4	Standard
ENST00000649621.1	Ensembl	ENSP00000497644.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Uricosurics Pathway, Pharmacodynamics
Metabolism
Nicotinamide salvaging
Nicotinate metabolism
Metabolism of water-soluble vitamins and cofactors

Biological Process

organic cation transport
urate transport
NAD biosynthesis via nicotinamide riboside salvage pathway
transmembrane transport
nicotinate transport

Molecular Function

organic cation transmembrane transporter activity
nicotinate transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane
apical plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000311856
Coding exons: 10
Length: 12504
Individuals with no LoFs: 125579
Homozygous LoFs: 0
Heterozygous LoFs: 169
Defined: 125748
p: 0.000672

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.109	330	336	0.983	0.0000202	3551
Missense (PolyPhen)		84	97.548	0.86111		1073
Synonymous	-0.430	148	141	1.05	0.00000881	1175
Loss of Function	0.193	21	22.0	0.956	0.00000104	230

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00098	0.00098	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00076	0.00076	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00079	0.00078	rare
South Asian	0.00052	0.00052	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.661
RVIS EVS: -0.26
RVIS percentile EVS: 34.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.333

Gene Damage Prediction

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