SLC22A17

solute carrier family 22 member 17, the group of Solute carrier family 22

Basic information

Region (hg38): 14:23346313-23352912

Links

ENSG00000092096 ∙ NCBI:51310 ∙ OMIM:611461 ∙ HGNC:23095 ∙ Uniprot:Q8WUG5 ∙ 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 SLC22A17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A17 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				2	1	3
missense			36			36
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	37	2	1

Variants in SLC22A17

This is a list of pathogenic ClinVar variants found in the SLC22A17 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-23346670-G-A		not specified	Uncertain significance (Mar 01, 2024)
14-23346713-G-A		not specified	Uncertain significance (Nov 13, 2023)
14-23346716-G-C		not specified	Uncertain significance (Mar 20, 2023)
14-23346718-A-G		not specified	Uncertain significance (Dec 22, 2023)
14-23346728-G-A		not specified	Uncertain significance (Dec 31, 2023)
14-23346733-C-T		not specified	Uncertain significance (Jul 14, 2022)
14-23346773-G-A		not specified	Uncertain significance (Nov 18, 2022)
14-23346784-G-A		not specified	Uncertain significance (Mar 29, 2024)
14-23346800-T-C		not specified	Uncertain significance (Jul 12, 2023)
14-23346872-G-T		not specified	Uncertain significance (Dec 01, 2022)
14-23346884-C-T		not specified	Uncertain significance (Feb 06, 2024)
14-23347132-G-A		not specified	Uncertain significance (Feb 15, 2023)
14-23347132-G-T		not specified	Uncertain significance (Nov 09, 2023)
14-23347197-G-A		not specified	Uncertain significance (Jun 21, 2023)
14-23347198-C-T		not specified	Uncertain significance (Feb 27, 2023)
14-23347461-T-A		not specified	Uncertain significance (Mar 08, 2024)
14-23347555-A-G		not specified	Uncertain significance (Feb 15, 2023)
14-23347616-A-T		not specified	Uncertain significance (Oct 22, 2021)
14-23347634-C-T		not specified	Uncertain significance (Jan 04, 2024)
14-23347711-C-T		not specified	Uncertain significance (Aug 28, 2023)
14-23347894-G-C		not specified	Uncertain significance (Mar 11, 2024)
14-23347909-A-G		not specified	Uncertain significance (Jan 26, 2023)
14-23347916-T-G		not specified	Uncertain significance (Jul 06, 2021)
14-23347964-A-T		not specified	Uncertain significance (Oct 17, 2023)
14-23348218-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A17	protein_coding	protein_coding	ENST00000397267	9	6607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0106	0.989	125731	0	12	125743	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	246	317	0.776	0.0000187	3366
Missense in Polyphen		95	146.58	0.6481		1462
Synonymous	0.739	127	138	0.920	0.00000783	1231
Loss of Function	3.11	8	24.7	0.324	0.00000158	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000481	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor for LCN2 (24p3) that plays a key role in iron homeostasis and transport. Able to bind iron-bound LCN2 (holo-24p3), followed by internalization of holo-24p3 and release of iron, thereby increasing intracellular iron concentration and leading to inhibition of apoptosis. Also binds iron-free LCN2 (apo-24p3), followed by internalization of apo-24p3 and its association with an intracellular siderophore, leading to iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration and resulting in apoptosis (By similarity). {ECO:0000250}.
• Pathway: Transport of small molecules;Iron uptake and transport (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.262
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.389
• hipred: N
• hipred_score: 0.420
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.361

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a17

Gene ontology

• Biological process: cellular iron ion homeostasis;siderophore transport;transmembrane transport
• Cellular component: vacuolar membrane;plasma membrane;integral component of plasma membrane;integral component of organelle membrane
• Molecular function: transmembrane signaling receptor activity;transmembrane transporter activity