SULT1C3

protein-coding

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

Gene summary

Enables 3'-phosphoadenosine 5'-phosphosulfate binding activity and sulfotransferase activity. Involved in 3'-phosphoadenosine 5'-phosphosulfate metabolic process; cholesterol metabolic process; and xenobiotic metabolic process. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001320878.2

Inheritance

—

ClinVar variants

U:39B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.54

Max pathogenic AF

—

Genomic locus

chr2:108,239,968-108,265,351

External References & Databases

Ensembl (ENSG00000196228)

Transcript & Mutation Effects

hg38 • Region Span ~25.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SULT1C3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001320878.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			39 clinvar	1 clinvar	2 clinvar	42
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	1	3	43

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001320878.2	RefSeq	NP_001307807.1	7	MANE Select
ENST00000681802.2	Ensembl	ENSP00000505748.1	7	MANE Select
NM_001008743.3	RefSeq	NP_001008743.1	7	Standard
ENST00000329106.3	Ensembl	ENSP00000333310.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Sulfation Biotransformation Reaction
Metapathway biotransformation Phase I and II

Biological Process

sulfur compound metabolic process

Molecular Function

alcohol sulfotransferase activity
aryl sulfotransferase activity

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329106
Coding exons: 7
Length: 18157
Individuals with no LoFs: 125643
Homozygous LoFs: 0
Heterozygous LoFs: 81
Defined: 125724
p: 0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.200	151	158	0.955	0.00000770	2039
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00022	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00056	0.00055	rare
European (Non-Finnish)	0.00047	0.00046	rare
South Asian	0.00014	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0829

Intolerance Scores

LoFtool: 0.548
RVIS EVS: 1.6
RVIS percentile EVS: 95.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0568

Gene Damage Prediction

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