SULT1C2

sulfotransferase family 1C member 2, the group of Sulfotransferases, cytosolic

Basic information

Region (hg38): 2:108288639-108309915

Previous symbols: [ "SULT1C1" ]

Links

ENSG00000198203 ∙ NCBI:6819 ∙ OMIM:602385 ∙ HGNC:11456 ∙ Uniprot:O00338 ∙ 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 SULT1C2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SULT1C2 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
missense			19	2	2	23
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	19	2	4

Variants in SULT1C2

This is a list of pathogenic ClinVar variants found in the SULT1C2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-108293678-C-T		not specified	Uncertain significance (Sep 04, 2024)
2-108293716-G-C		not specified	Uncertain significance (Jul 12, 2023)
2-108293773-G-A		not specified	Uncertain significance (Apr 13, 2023)
2-108293799-C-T			Benign (Jul 13, 2018)
2-108294279-G-A			Benign (Aug 06, 2018)
2-108294322-T-C		not specified	Uncertain significance (Jun 21, 2021)
2-108294325-T-C		not specified	Uncertain significance (Feb 28, 2023)
2-108298574-A-G			Likely benign (Feb 01, 2025)
2-108300871-G-A		not specified	Uncertain significance (Jan 04, 2022)
2-108300927-A-G		not specified	Uncertain significance (Sep 04, 2024)
2-108304580-T-C			Likely benign (Mar 01, 2023)
2-108304590-G-A		not specified	Uncertain significance (Aug 08, 2022)
2-108304609-G-A		not specified	Uncertain significance (Oct 22, 2021)
2-108304616-T-C		not specified	Uncertain significance (Jan 02, 2025)
2-108304622-C-A		not specified	Uncertain significance (Jan 19, 2024)
2-108304641-A-C		not specified	Uncertain significance (Aug 08, 2022)
2-108304656-C-G		not specified	Uncertain significance (Jul 09, 2021)
2-108304687-C-A		not specified	Uncertain significance (Jul 06, 2022)
2-108304692-A-G		not specified	Likely benign (May 03, 2023)
2-108304705-G-A			Benign (Aug 09, 2018)
2-108305181-G-A		not specified	Uncertain significance (Jul 19, 2023)
2-108305217-T-C		not specified	Uncertain significance (Dec 20, 2023)
2-108305433-C-T			Benign (Jul 18, 2018)
2-108305461-A-C		not specified	Uncertain significance (Feb 27, 2025)
2-108305499-A-C		not specified	Uncertain significance (Jul 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SULT1C2	protein_coding	protein_coding	ENST00000326853	8	21277

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.65e-10	0.151	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.175	165	159	1.04	0.00000788	2055
Missense in Polyphen		68	63.892	1.0643		820
Synonymous	0.919	45	53.6	0.840	0.00000284	526
Loss of Function	0.476	16	18.2	0.879	9.83e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000361
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.000220	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000176	0.000158
Middle Eastern	0.000220	0.000217
South Asian	0.000523	0.000523
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).
• Pathway: Vitamin D Receptor 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: 0.360
• rvis_EVS: 1.59
• rvis_percentile_EVS: 95.84

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.169

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.723

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sult1c2

Gene ontology

• Biological process: amine metabolic process;3'-phosphoadenosine 5'-phosphosulfate metabolic process;sulfation
• Cellular component: cytoplasm;cytosol
• Molecular function: aryl sulfotransferase activity;protein binding;sulfotransferase activity