SULT1C3

sulfotransferase family 1C member 3, the group of Sulfotransferases, cytosolic

Basic information

Region (hg38): 2:108239968-108265351

Links

ENSG00000196228 ∙ NCBI:442038 ∙ OMIM:617151 ∙ HGNC:33543 ∙ Uniprot:Q6IMI6 ∙ 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 SULT1C3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SULT1C3 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			23	1	2	26
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	3

Variants in SULT1C3

This is a list of pathogenic ClinVar variants found in the SULT1C3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-108247199-C-T		not specified	Uncertain significance (Dec 07, 2023)
2-108247205-T-C		not specified	Uncertain significance (Apr 06, 2022)
2-108247214-A-C		not specified	Uncertain significance (Dec 03, 2024)
2-108247235-A-G		not specified	Uncertain significance (Mar 13, 2023)
2-108247271-T-A		not specified	Uncertain significance (Sep 30, 2024)
2-108247302-G-A		not specified	Benign (Mar 28, 2016)
2-108247329-G-C		not specified	Uncertain significance (Sep 16, 2021)
2-108247349-C-A		not specified	Uncertain significance (Aug 14, 2023)
2-108252371-C-A		not specified	Uncertain significance (Nov 14, 2023)
2-108252394-A-G		not specified	Uncertain significance (Mar 26, 2024)
2-108252398-T-G		not specified	Uncertain significance (Oct 12, 2022)
2-108252420-G-C		not specified	Uncertain significance (Nov 20, 2023)
2-108252454-G-A			Benign (Jul 16, 2018)
2-108253356-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-108253380-C-A		not specified	Uncertain significance (Jan 16, 2024)
2-108253437-T-A		not specified	Uncertain significance (Nov 06, 2023)
2-108255602-T-C		not specified	Uncertain significance (Aug 09, 2021)
2-108255687-T-C		not specified	Uncertain significance (Nov 30, 2022)
2-108255690-C-G		not specified	Uncertain significance (May 30, 2024)
2-108255692-G-A		not specified	Uncertain significance (Sep 03, 2024)
2-108255692-G-C		not specified	Uncertain significance (Sep 08, 2024)
2-108258739-G-A		not specified	Uncertain significance (Mar 01, 2023)
2-108258743-G-A		not specified	Uncertain significance (Aug 28, 2024)
2-108258789-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-108258789-G-T		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SULT1C3	protein_coding	protein_coding	ENST00000329106	7	18157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.43e-18	0.000215	125643	0	81	125724	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.200	151	158	0.955	0.00000770	2039
Missense in Polyphen		36	52.113	0.69081		744
Synonymous	-0.296	59	56.2	1.05	0.00000313	508
Loss of Function	-1.89	22	14.3	1.54	6.04e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000408	0.000401
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000558	0.000554
European (Non-Finnish)	0.000469	0.000457
Middle Eastern	0.000109	0.000109
South Asian	0.000140	0.000131
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor and has low sulphotransferase activity towards various substrates with alcohol groups (in vitro). May catalyze the sulfate conjugation of xenobiotic compounds and endogenous substrates. {ECO:0000269|PubMed:17425406, ECO:0000269|PubMed:17936463}.
• Pathway: Sulfation Biotransformation Reaction;Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.0829

Intolerance Scores

• loftool: 0.548
• rvis_EVS: 1.6
• rvis_percentile_EVS: 95.87

Haploinsufficiency Scores

• pHI: 0.0283
• hipred: N
• hipred_score: 0.190

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0568

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sult1c1
• Phenotype: skeleton phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: sulfur compound metabolic process
• Cellular component: cytoplasm
• Molecular function: alcohol sulfotransferase activity;aryl sulfotransferase activity