SULT1C4

sulfotransferase family 1C member 4, the group of Sulfotransferases, cytosolic

Basic information

Region (hg38): 2:108377911-108388989

Previous symbols: [ "SULT1C2" ]

Links

ENSG00000198075 ∙ NCBI:27233 ∙ OMIM:608357 ∙ HGNC:11457 ∙ Uniprot:O75897 ∙ 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 SULT1C4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SULT1C4 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in SULT1C4

This is a list of pathogenic ClinVar variants found in the SULT1C4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-108378347-C-T		not specified	Uncertain significance (Feb 07, 2023)
2-108378350-G-A		not specified	Uncertain significance (Nov 08, 2022)
2-108378356-G-C		not specified	Uncertain significance (Dec 06, 2022)
2-108378406-G-C		not specified	Uncertain significance (Jan 04, 2022)
2-108378408-G-A		not specified	Uncertain significance (May 16, 2023)
2-108378420-C-G		not specified	Uncertain significance (Nov 09, 2021)
2-108378420-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-108378426-A-G		not specified	Uncertain significance (Mar 23, 2022)
2-108381786-T-G		not specified	Uncertain significance (Jul 13, 2022)
2-108381789-A-T		not specified	Uncertain significance (Feb 28, 2023)
2-108381809-G-A		not specified	Uncertain significance (Nov 09, 2024)
2-108381828-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-108381867-A-G		not specified	Uncertain significance (Sep 16, 2021)
2-108382415-C-A		not specified	Uncertain significance (Dec 13, 2021)
2-108382441-T-C		not specified	Uncertain significance (Nov 01, 2022)
2-108383118-A-G		not specified	Uncertain significance (Dec 20, 2023)
2-108383147-C-G		not specified	Uncertain significance (Jan 09, 2023)
2-108383213-G-A		not specified	Uncertain significance (May 09, 2023)
2-108383419-G-C		not specified	Uncertain significance (Dec 16, 2021)
2-108383475-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-108383476-G-A		not specified	Uncertain significance (May 24, 2023)
2-108386212-G-C		not specified	Uncertain significance (Jan 09, 2024)
2-108386237-A-G		not specified	Uncertain significance (May 25, 2022)
2-108387349-A-G		not specified	Uncertain significance (Dec 19, 2023)
2-108387386-A-G		not specified	Uncertain significance (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SULT1C4	protein_coding	protein_coding	ENST00000272452	7	10147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000497	0.665	125661	1	83	125745	0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	146	154	0.945	0.00000764	2018
Missense in Polyphen		57	54.984	1.0367		712
Synonymous	0.262	51	53.4	0.954	0.00000285	511
Loss of Function	1.01	10	14.1	0.710	5.95e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000443	0.000434
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000725	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00210	0.00206
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of drugs, xenobiotic compounds, hormones, and neurotransmitters. May be involved in the activation of carcinogenic hydroxylamines. Shows activity towards p-nitrophenol and N-hydroxy-2-acetylamino-fluorene (N-OH-2AAF). {ECO:0000269|PubMed:17425406}.
• Pathway: Sulfation Biotransformation Reaction;Metapathway biotransformation Phase I and II;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.532
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.279

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: ethanol catabolic process;3'-phosphoadenosine 5'-phosphosulfate metabolic process;sulfation
• Cellular component: cellular_component;cytosol
• Molecular function: aryl sulfotransferase activity;sulfotransferase activity