SLCO6A1

solute carrier organic anion transporter family member 6A1, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 5:102371773-102499016

Links

ENSG00000205359 ∙ NCBI:133482 ∙ OMIM:613365 ∙ HGNC:23613 ∙ Uniprot:Q86UG4 ∙ 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 SLCO6A1 gene.

• Inborn genetic diseases (20 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO6A1 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	3	5
missense			17	4	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	6	4

Variants in SLCO6A1

This is a list of pathogenic ClinVar variants found in the SLCO6A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-102373370-T-C			Benign (Jul 18, 2018)
5-102373384-T-C			Likely benign (Jun 14, 2018)
5-102373432-G-A		not specified	Uncertain significance (May 16, 2022)
5-102388723-T-A		not specified	Uncertain significance (Oct 20, 2023)
5-102388755-T-C			Likely benign (Jun 01, 2022)
5-102388783-G-C		not specified	Likely benign (Jun 21, 2021)
5-102399571-C-T		not specified	Likely benign (Oct 03, 2023)
5-102399669-C-G			Benign (Jul 21, 2018)
5-102413024-C-G		not specified	Uncertain significance (Aug 21, 2023)
5-102419851-C-A		not specified	Uncertain significance (Dec 28, 2023)
5-102419862-G-A		not specified	Uncertain significance (Jan 12, 2024)
5-102419881-T-C		not specified	Uncertain significance (Jun 13, 2022)
5-102438649-A-G		not specified	Uncertain significance (Dec 05, 2023)
5-102438671-T-C		not specified	Uncertain significance (Jul 05, 2023)
5-102458390-C-G		not specified	Uncertain significance (Sep 27, 2021)
5-102458393-C-T		not specified	Uncertain significance (May 11, 2022)
5-102458403-C-A		not specified	Uncertain significance (Oct 04, 2022)
5-102458463-A-G			Benign (Jul 26, 2018)
5-102458465-G-A		not specified	Uncertain significance (May 27, 2022)
5-102458482-C-T		not specified	Uncertain significance (Feb 06, 2023)
5-102458483-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-102459665-T-C		not specified	Uncertain significance (Dec 20, 2021)
5-102459702-T-C			Likely benign (Jul 11, 2018)
5-102459704-C-A		not specified	Uncertain significance (Dec 16, 2022)
5-102475733-A-T		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO6A1	protein_coding	protein_coding	ENST00000506729	13	127235

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.88e-11	0.704	125676	0	11	125687	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.511	355	383	0.926	0.0000203	4629
Missense in Polyphen		96	108.88	0.88171		1411
Synonymous	0.356	130	135	0.961	0.00000731	1406
Loss of Function	1.55	21	30.2	0.696	0.00000135	447

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000267	0.000250
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000276	0.0000264
Middle Eastern	0.000116	0.000109
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.721

Intolerance Scores

• loftool: 0.664
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94.05

Haploinsufficiency Scores

• pHI: 0.0157
• hipred: N
• hipred_score: 0.132

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0421

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco6d1

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