SLC22A13

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

Basic information

Region (hg38): 3:38265812-38278757

Previous symbols: [ "ORCTL3" ]

Links

ENSG00000172940 ∙ NCBI:9390 ∙ OMIM:604047 ∙ HGNC:8494 ∙ Uniprot:Q9Y226 ∙ 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 SLC22A13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A13 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				1		1
missense			40	5	1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	6	1

Variants in SLC22A13

This is a list of pathogenic ClinVar variants found in the SLC22A13 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-38265898-A-T		not specified	Uncertain significance (Apr 05, 2023)
3-38265907-G-A			Benign (Nov 01, 2022)
3-38266008-T-G		not specified	Uncertain significance (Jan 21, 2025)
3-38266018-C-A		not specified	Uncertain significance (Jan 19, 2024)
3-38266045-T-C		not specified	Uncertain significance (May 09, 2023)
3-38266165-G-A			Likely benign (Feb 01, 2025)
3-38266188-G-C		not specified	Uncertain significance (Aug 17, 2021)
3-38274291-G-A		not specified	Uncertain significance (Jul 05, 2023)
3-38274326-A-G		not specified	Uncertain significance (Dec 04, 2024)
3-38274371-G-A		not specified	Uncertain significance (Feb 02, 2024)
3-38274374-C-T		not specified	Likely benign (Feb 13, 2024)
3-38274630-C-T		not specified	Likely benign (Jan 16, 2025)
3-38274663-C-T		not specified	Likely benign (May 10, 2024)
3-38274725-G-A		not specified	Likely benign (Oct 05, 2023)
3-38275019-C-T		not specified	Uncertain significance (May 16, 2024)
3-38275046-A-G		not specified	Uncertain significance (Dec 25, 2024)
3-38275058-G-T		not specified	Uncertain significance (Nov 10, 2024)
3-38275081-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-38275093-C-T		not specified	Uncertain significance (Jul 16, 2021)
3-38275094-G-A		not specified	Uncertain significance (Jan 02, 2024)
3-38275120-G-A		not specified	Uncertain significance (Oct 29, 2024)
3-38275124-C-T		not specified	Uncertain significance (Nov 09, 2024)
3-38275151-A-G		not specified	Uncertain significance (May 17, 2023)
3-38275386-G-A		not specified	Uncertain significance (Aug 02, 2021)
3-38275404-C-T		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A13	protein_coding	protein_coding	ENST00000311856	10	12504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.31e-14	0.0280	125579	0	169	125748	0.000672

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.109	330	336	0.983	0.0000202	3551
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00148	0.00148
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000762	0.000761
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.000788	0.000783
Middle Eastern	0.000762	0.000761
South Asian	0.000523	0.000523
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

• Pathway: Uricosurics Pathway, Pharmacodynamics;Metabolism;Nicotinamide salvaging;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.661
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.93

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.170
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.333

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a13

Gene ontology

• Biological process: organic cation transport;urate transport;NAD biosynthesis via nicotinamide riboside salvage pathway;transmembrane transport;nicotinate transport
• Cellular component: plasma membrane;integral component of plasma membrane;apical plasma membrane;extracellular exosome
• Molecular function: organic cation transmembrane transporter activity;nicotinate transmembrane transporter activity