SLCO5A1

solute carrier organic anion transporter family member 5A1, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 8:69667046-69834978

Previous symbols: [ "SLC21A15" ]

Links

ENSG00000137571 ∙ NCBI:81796 ∙ OMIM:613543 ∙ HGNC:19046 ∙ Uniprot:Q9H2Y9 ∙ 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 SLCO5A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO5A1 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	47	13	62
missense			134	9	6	149
nonsense			5			5
start loss						0
frameshift			5			5
inframe indel			4			4
splice donor/acceptor (+/-2bp)			1			1
splice region			5	3		8
non coding			2	5	6	13
Total	0	0	153	61	25

Variants in SLCO5A1

This is a list of pathogenic ClinVar variants found in the SLCO5A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-69672886-A-C			Uncertain significance (Sep 07, 2022)
8-69672888-G-A		not specified	Uncertain significance (Feb 23, 2023)
8-69672892-C-CG			Uncertain significance (Oct 15, 2023)
8-69672895-G-T		not specified	Uncertain significance (Nov 09, 2024)
8-69672897-C-A			Uncertain significance (Nov 16, 2023)
8-69672904-C-A			Uncertain significance (Nov 15, 2023)
8-69672918-G-T			Uncertain significance (Aug 30, 2022)
8-69672924-G-A			Uncertain significance (May 26, 2023)
8-69672934-C-T			Uncertain significance (Aug 04, 2023)
8-69672944-G-A			Benign (Dec 23, 2020)
8-69672951-G-A			Uncertain significance (Mar 17, 2023)
8-69672951-G-T			Uncertain significance (Aug 09, 2022)
8-69672952-G-A			Uncertain significance (May 22, 2023)
8-69672971-C-G			Uncertain significance (Jul 07, 2023)
8-69672975-A-G			Uncertain significance (Jul 22, 2023)
8-69672979-C-CT			Uncertain significance (Dec 03, 2021)
8-69672988-G-A			Benign (Jan 23, 2024)
8-69672989-G-T			Likely benign (Aug 04, 2023)
8-69672991-C-T			Uncertain significance (Sep 02, 2021)
8-69672999-T-C			Uncertain significance (Jun 14, 2023)
8-69673001-G-A			Likely benign (Aug 17, 2023)
8-69673015-G-C			Uncertain significance (Jul 06, 2022)
8-69673030-G-C			Uncertain significance (Jan 19, 2024)
8-69673038-C-G			Uncertain significance (Jul 06, 2022)
8-69673044-C-G			Uncertain significance (Nov 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO5A1	protein_coding	protein_coding	ENST00000260126	9	168018

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000154	0.998	125641	0	107	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.903	443	500	0.886	0.0000287	5496
Missense in Polyphen		84	137.3	0.61181		1434
Synonymous	1.04	191	210	0.909	0.0000142	1743
Loss of Function	2.77	15	31.9	0.470	0.00000159	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00147
Ashkenazi Jewish	0.00	0.00
East Asian	0.000285	0.000272
Finnish	0.000888	0.000878
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000285	0.000272
South Asian	0.000131	0.000131
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.772
• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.34

Haploinsufficiency Scores

• pHI: 0.445
• hipred: N
• hipred_score: 0.498
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.184

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco5a1

Gene ontology

• Biological process: sodium-independent organic anion transport;transmembrane transport
• Cellular component: integral component of plasma membrane
• Molecular function: sodium-independent organic anion transmembrane transporter activity