SULT4A1

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

Basic information

Region (hg38): 22:43824509-43862513

Links

ENSG00000130540 ∙ NCBI:25830 ∙ OMIM:608359 ∙ HGNC:14903 ∙ Uniprot:Q9BR01 ∙ 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 SULT4A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SULT4A1 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				2		2
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in SULT4A1

This is a list of pathogenic ClinVar variants found in the SULT4A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-43826042-T-G		not specified	Uncertain significance (Jan 18, 2025)
22-43826072-T-G		not specified	Uncertain significance (May 06, 2024)
22-43829062-C-T		not specified	Uncertain significance (May 03, 2023)
22-43829085-G-A		not specified	Likely benign (Aug 04, 2024)
22-43829122-G-A		not specified	Uncertain significance (Feb 19, 2025)
22-43833641-C-T		not specified	Uncertain significance (Mar 22, 2022)
22-43833672-C-T		not specified	Uncertain significance (Nov 16, 2022)
22-43833712-C-A		not specified	Uncertain significance (Oct 16, 2024)
22-43838887-C-T		not specified	Uncertain significance (Sep 16, 2021)
22-43838960-C-T		not specified	Uncertain significance (Dec 12, 2024)
22-43839958-T-C		not specified	Uncertain significance (Oct 05, 2023)
22-43840010-G-A		not specified	Uncertain significance (Feb 26, 2025)
22-43841844-G-A			Likely benign (Apr 03, 2018)
22-43841852-C-T		not specified	Uncertain significance (Jul 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SULT4A1	protein_coding	protein_coding	ENST00000330884	7	38010

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.966	0.0344	125733	0	2	125735	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	74	172	0.430	0.00000992	1859
Missense in Polyphen		13	43.423	0.29938		478
Synonymous	0.200	68	70.1	0.970	0.00000430	508
Loss of Function	3.33	1	14.9	0.0672	8.19e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical sulfotransferase family member with very low affinity for 3'-phospho-5'-adenylyl sulfate (PAPS) and very low catalytic activity towards L-triiodothyronine, thyroxine, estrone, p-nitrophenol, 2-naphthylamine, and 2-beta-naphthol. May have a role in the metabolism of drugs and neurotransmitters in the CNS. {ECO:0000269|PubMed:17425406}.
• Pathway: Sulfation Biotransformation Reaction;Metapathway biotransformation Phase I and II;Phase II - Conjugation of compounds;Tyrosine metabolism;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules (Consensus)

Recessive Scores

• pRec: 0.271

Intolerance Scores

• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.189
• hipred: Y
• hipred_score: 0.806
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sult4a1

Zebrafish Information Network

• Gene name: sult4a1
• Affected structure: adult behavior
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Biological process: biological_process;steroid metabolic process;3'-phosphoadenosine 5'-phosphosulfate metabolic process
• Cellular component: cytosol
• Molecular function: aryl sulfotransferase activity;protein binding;sulfotransferase activity;identical protein binding