SLCO4A1

solute carrier organic anion transporter family member 4A1, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 20:62642503-62685785

Previous symbols: [ "SLC21A12" ]

Links

ENSG00000101187 ∙ NCBI:28231 ∙ OMIM:612436 ∙ HGNC:10953 ∙ Uniprot:Q96BD0 ∙ 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 SLCO4A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO4A1 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						0
missense			49	5		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	5	0

Variants in SLCO4A1

This is a list of pathogenic ClinVar variants found in the SLCO4A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-62656462-T-A		not specified	Likely benign (Jun 06, 2023)
20-62656485-C-T		not specified	Uncertain significance (Dec 02, 2022)
20-62656704-G-A		not specified	Uncertain significance (Dec 21, 2022)
20-62656710-T-C		not specified	Uncertain significance (Jun 10, 2024)
20-62656786-C-T		not specified	Uncertain significance (Dec 15, 2023)
20-62656791-G-A		not specified	Uncertain significance (Jan 31, 2023)
20-62656852-G-A		not specified	Uncertain significance (Jan 17, 2023)
20-62656881-G-A		not specified	Uncertain significance (Apr 26, 2024)
20-62656888-T-C		not specified	Uncertain significance (Jan 22, 2024)
20-62656893-A-G		not specified	Uncertain significance (Feb 28, 2023)
20-62656989-C-T		not specified	Uncertain significance (Oct 02, 2023)
20-62656999-C-T		not specified	Uncertain significance (Nov 09, 2023)
20-62657032-C-T		not specified	Uncertain significance (Apr 13, 2022)
20-62657034-G-A		not specified	Uncertain significance (Oct 04, 2022)
20-62657091-G-A		not specified	Likely benign (May 02, 2023)
20-62657094-G-A		not specified	Uncertain significance (Dec 19, 2022)
20-62657097-G-T		not specified	Uncertain significance (Sep 22, 2023)
20-62657169-G-T		not specified	Uncertain significance (May 09, 2022)
20-62657175-G-A		not specified	Uncertain significance (Nov 10, 2022)
20-62657193-C-A		not specified	Uncertain significance (Jan 24, 2024)
20-62657239-C-T		not specified	Uncertain significance (Sep 27, 2021)
20-62658692-C-A		not specified	Uncertain significance (May 27, 2022)
20-62658733-G-A		not specified	Uncertain significance (Sep 19, 2022)
20-62658764-G-A		not specified	Likely benign (May 03, 2023)
20-62658766-C-T		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO4A1	protein_coding	protein_coding	ENST00000217159	11	43341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-10	0.738	125563	0	182	125745	0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.430	437	463	0.944	0.0000305	4594
Missense in Polyphen		147	166.33	0.8838		1724
Synonymous	-1.09	244	223	1.09	0.0000174	1527
Loss of Function	1.56	20	29.1	0.688	0.00000152	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000621	0.000621
Ashkenazi Jewish	0.00	0.00
East Asian	0.000387	0.000381
Finnish	0.00164	0.00153
European (Non-Finnish)	0.000939	0.000897
Middle Eastern	0.000387	0.000381
South Asian	0.000435	0.000425
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the Na(+)-independent transport of organic anions such as the thyroid hormones T3 (triiodo-L-thyronine), T4 (thyroxine) and rT3, and of estrone-3-sulfate and taurocholate.
• Pathway: Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Prostaglandin formation from arachidonate;Bile acid biosynthesis;Transport of organic anions (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.726
• rvis_EVS: -1.32
• rvis_percentile_EVS: 4.78

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.264
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco4a1

Gene ontology

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