SLCO4C1

solute carrier organic anion transporter family member 4C1, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 5:102233986-102296284

Links

ENSG00000173930 ∙ NCBI:353189 ∙ OMIM:609013 ∙ HGNC:23612 ∙ Uniprot:Q6ZQN7 ∙ 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 SLCO4C1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO4C1 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			21	4	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	21	6	1

Variants in SLCO4C1

This is a list of pathogenic ClinVar variants found in the SLCO4C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-102236860-A-G			Likely benign (May 08, 2018)
5-102236873-T-C		not specified	Uncertain significance (May 28, 2024)
5-102236899-A-C		not specified	Uncertain significance (Oct 03, 2022)
5-102236949-G-A		not specified	Likely benign (Jan 03, 2024)
5-102237003-A-G		not specified	Uncertain significance (Sep 26, 2023)
5-102237015-A-G		not specified	Uncertain significance (Jan 26, 2022)
5-102239272-C-T		not specified	Uncertain significance (May 14, 2024)
5-102239281-T-A		not specified	Uncertain significance (Sep 17, 2021)
5-102239289-T-G		not specified	Uncertain significance (Jun 05, 2024)
5-102239367-A-G		not specified	Uncertain significance (Mar 15, 2024)
5-102247339-G-A		not specified	Uncertain significance (Nov 17, 2022)
5-102247409-T-G		not specified	Uncertain significance (May 20, 2024)
5-102249727-A-G		not specified	Uncertain significance (May 13, 2022)
5-102249735-G-A		not specified	Likely benign (May 20, 2024)
5-102249744-C-A		not specified	Uncertain significance (Apr 04, 2024)
5-102249748-T-C		not specified	Uncertain significance (Dec 15, 2022)
5-102249762-G-T		not specified	Uncertain significance (Dec 21, 2023)
5-102257125-A-G		not specified	Uncertain significance (Dec 09, 2023)
5-102257178-A-C		not specified	Uncertain significance (Apr 08, 2024)
5-102257226-G-C		not specified	Uncertain significance (Apr 09, 2024)
5-102257244-C-A		not specified	Uncertain significance (Feb 15, 2023)
5-102258045-T-C		not specified	Uncertain significance (Nov 20, 2023)
5-102258048-A-G		not specified	Uncertain significance (Dec 14, 2023)
5-102260274-C-T		not specified	Likely benign (Oct 03, 2022)
5-102260309-T-A			Benign (Jan 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO4C1	protein_coding	protein_coding	ENST00000310954	13	62564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-8	0.983	125666	0	81	125747	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.243	378	365	1.04	0.0000171	4661
Missense in Polyphen		109	113.22	0.96272		1388
Synonymous	0.757	127	138	0.918	0.00000679	1448
Loss of Function	2.28	18	31.9	0.565	0.00000158	424

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000657	0.000657
Ashkenazi Jewish	0.00	0.00
East Asian	0.000605	0.000598
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000339	0.000334
Middle Eastern	0.000605	0.000598
South Asian	0.000409	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Organic anion transporter, capable of transporting pharmacological substances such as digoxin, ouabain, thyroxine, methotrexate and cAMP. May participate in the regulation of membrane transport of ouabain. Involved in the uptake of the dipeptidyl peptidase-4 inhibitor sitagliptin and hence may play a role in its transport into and out of renal proximal tubule cells. May be involved in the first step of the transport pathway of digoxin and various compounds into the urine in the kidney. May be involved in sperm maturation by enabling directed movement of organic anions and compounds within or between cells. This ion- transporting process is important to maintain the strict epididymal homeostasis necessary for sperm maturation. May have a role in secretory functions since seminal vesicle epithelial cells are assumed to secrete proteins involved in decapacitation by modifying surface proteins to facilitate the acquisition of the ability to fertilize the egg. {ECO:0000250|UniProtKB:Q8BGD4, ECO:0000269|PubMed:14993604, ECO:0000269|PubMed:17314201}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Transport of organic anions (Consensus)

Recessive Scores

• pRec: 0.0838

Intolerance Scores

• loftool: 0.719
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.15

Haploinsufficiency Scores

• pHI: 0.280
• hipred: N
• hipred_score: 0.231
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.345

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco4c1

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation;sodium-independent organic anion transport;neutrophil degranulation;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;basolateral plasma membrane;azurophil granule membrane;specific granule membrane;extracellular exosome
• Molecular function: sodium-independent organic anion transmembrane transporter activity