SLCO1C1

solute carrier organic anion transporter family member 1C1, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 12:20695332-20753386

Previous symbols: [ "SLC21A14" ]

Links

ENSG00000139155 ∙ NCBI:53919 ∙ OMIM:613389 ∙ HGNC:13819 ∙ Uniprot:Q9NYB5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLCO1C1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO1C1 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				1	1	2
missense			24	1	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	25	2	4

Variants in SLCO1C1

This is a list of pathogenic ClinVar variants found in the SLCO1C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-20701345-T-A			Uncertain significance (Jan 01, 2023)
12-20701395-G-C		not specified	Uncertain significance (Apr 04, 2024)
12-20705963-A-G		not specified	Uncertain significance (Dec 15, 2022)
12-20705967-C-T		not specified	Uncertain significance (Dec 27, 2023)
12-20705987-G-A		not specified	Uncertain significance (Apr 06, 2024)
12-20711444-C-A		not specified	Uncertain significance (Jan 26, 2023)
12-20711503-A-G		not specified	Uncertain significance (Oct 06, 2022)
12-20715279-T-A		not specified	Uncertain significance (Sep 12, 2023)
12-20715279-T-C		not specified	Uncertain significance (Jun 26, 2023)
12-20717186-C-T		not specified	Uncertain significance (May 15, 2024)
12-20717191-T-A		not specified	Uncertain significance (Aug 21, 2023)
12-20717214-T-G		not specified	Uncertain significance (Feb 14, 2023)
12-20721830-C-T		not specified	Uncertain significance (Aug 09, 2021)
12-20721838-G-T		not specified	Uncertain significance (Sep 25, 2023)
12-20721869-G-C		not specified	Uncertain significance (Dec 30, 2023)
12-20721879-T-A		not specified	Uncertain significance (Mar 04, 2024)
12-20721938-A-G		not specified	Uncertain significance (May 18, 2022)
12-20722030-A-C		not specified	Uncertain significance (Jan 27, 2022)
12-20722035-T-C		not specified	Uncertain significance (Sep 22, 2022)
12-20723104-C-G		not specified	Uncertain significance (Aug 12, 2021)
12-20723179-G-A		not specified	Uncertain significance (May 09, 2024)
12-20723189-C-T		not specified	Uncertain significance (Dec 05, 2022)
12-20723234-C-T			Benign (Dec 31, 2019)
12-20732951-G-A		not specified	Uncertain significance (Mar 19, 2024)
12-20732953-G-A		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO1C1	protein_coding	protein_coding	ENST00000381552	14	58032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.99e-12	0.755	125677	1	69	125747	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.477	392	366	1.07	0.0000167	4731
Missense in Polyphen		120	118.67	1.0112		1460
Synonymous	-0.446	137	131	1.05	0.00000623	1392
Loss of Function	1.69	23	33.5	0.686	0.00000150	468

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000870	0.000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.000348	0.000326
Finnish	0.0000987	0.0000924
European (Non-Finnish)	0.000306	0.000299
Middle Eastern	0.000348	0.000326
South Asian	0.000210	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the Na(+)-independent high affinity transport of organic anions such as the thyroid hormones thyroxine (T4) and rT3. Other potential substrates, such as triiodothyronine (T3), 17-beta-glucuronosyl estradiol, estrone-3-sulfate and sulfobromophthalein (BSP) are transported with much lower efficiency. May play a signifiant role in regulating T4 flux into and out of the brain (By similarity). {ECO:0000250}.
• Pathway: Thyroid hormone signaling pathway - Homo sapiens (human);Angiopoietin Like Protein 8 Regulatory Pathway;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Transport of organic anions (Consensus)

Recessive Scores

• pRec: 0.0890

Intolerance Scores

• loftool: 0.943
• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.690
• hipred: N
• hipred_score: 0.491
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.205

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco1c1
• Phenotype: normal phenotype; homeostasis/metabolism phenotype

Gene ontology

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