SULT2B1

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

Basic information

Region (hg38): 19:48552171-48599425

Links

ENSG00000088002 ∙ NCBI:6820 ∙ OMIM:604125 ∙ HGNC:11459 ∙ Uniprot:O00204 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ichthyosis, congenital, autosomal recessive 14 (Strong), mode of inheritance: AR
• lamellar ichthyosis (Supportive), mode of inheritance: AR
• ichthyosis, congenital, autosomal recessive 14 (Limited), mode of inheritance: AR
• ichthyosis, congenital, autosomal recessive 14 (Strong), mode of inheritance: AR
• ichthyosis, congenital, autosomal recessive 14 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ichthyosis, congenital, autosomal recessive 14	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	28575648

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SULT2B1 gene.

• not provided (35 variants)
• Ichthyosis, congenital, autosomal recessive 14 (8 variants)
• Inborn genetic diseases (7 variants)
• Autosomal recessive congenital ichthyosis 2 (3 variants)
• Autosomal recessive congenital ichthyosis 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SULT2B1 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				7	7	14
missense	2	2	9	6	5	24
nonsense						0
start loss						0
frameshift	1					1
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region			1	1	2	4
non coding					1	1
Total	4	2	10	13	13

Highest pathogenic variant AF is 0.0000329

Variants in SULT2B1

This is a list of pathogenic ClinVar variants found in the SULT2B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48552265-G-A		Inborn genetic diseases	Uncertain significance (Dec 06, 2021)
19-48552267-C-T			Benign/Likely benign (Feb 01, 2024)
19-48552268-G-A		Inborn genetic diseases	Uncertain significance (May 24, 2023)
19-48552270-G-A			Likely benign (May 02, 2018)
19-48552281-C-T		SULT2B1-related disorder	Benign (Mar 01, 2022)
19-48552325-T-A		Autosomal recessive congenital ichthyosis 2 • Ichthyosis, congenital, autosomal recessive 14	Pathogenic (Jul 01, 2016)
19-48575967-G-A		SULT2B1-related disorder	Benign (Sep 01, 2023)
19-48575989-C-T		SULT2B1-related disorder	Benign (Jan 29, 2024)
19-48576007-C-T			Likely benign (Oct 14, 2023)
19-48576021-T-C		SULT2B1-related disorder	Benign/Likely benign (Jan 02, 2024)
19-48576050-G-A		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
19-48576093-G-A		SULT2B1-related disorder	Likely benign (Aug 14, 2019)
19-48587213-C-T			Likely benign (Jul 30, 2023)
19-48587223-C-G		SULT2B1-related disorder	Benign (Dec 19, 2023)
19-48587246-G-A		Ichthyosis, congenital, autosomal recessive 14	Likely pathogenic (Jun 08, 2018)
19-48587291-C-T			Likely benign (Mar 01, 2023)
19-48587292-G-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
19-48587312-C-T		Ichthyosis, congenital, autosomal recessive 14	Likely pathogenic (Jun 08, 2018)
19-48587342-G-C		Inborn genetic diseases	Uncertain significance (Dec 09, 2023)
19-48587377-C-CA		Autosomal recessive congenital ichthyosis 2 • Ichthyosis, congenital, autosomal recessive 14	Pathogenic (Jul 01, 2016)
19-48587418-T-C		Inborn genetic diseases	Uncertain significance (May 09, 2023)
19-48591599-C-T		SULT2B1-related disorder	Benign (Jan 20, 2024)
19-48591611-G-A			Likely benign (Jan 09, 2019)
19-48591631-C-T		Autosomal recessive congenital ichthyosis 1 • Ichthyosis, congenital, autosomal recessive 14	Pathogenic (Jul 01, 2016)
19-48591686-G-A		SULT2B1-related disorder	Benign/Likely benign (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SULT2B1	protein_coding	protein_coding	ENST00000201586	7	47351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.436	0.563	125738	0	7	125745	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	187	235	0.796	0.0000153	2367
Missense in Polyphen		49	74.923	0.654		800
Synonymous	0.132	99	101	0.983	0.00000741	685
Loss of Function	2.74	3	14.1	0.213	5.99e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000376	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000337	0.0000327
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs and xenobiotic compounds. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Sulfates hydroxysteroids like DHEA. Isoform 1 preferentially sulfonates cholesterol, and isoform 2 avidly sulfonates pregnenolone but not cholesterol. Plays a role in epidermal cholesterol metabolism and in the regulation of epidermal proliferation and differentiation (PubMed:28575648). {ECO:0000269|PubMed:12145317, ECO:0000269|PubMed:28575648, ECO:0000269|PubMed:9799594}.
• Pathway: Steroid hormone biosynthesis - Homo sapiens (human);17-Beta Hydroxysteroid Dehydrogenase III Deficiency;Sulfate/Sulfite Metabolism;Sulfite oxidase deficiency;Androgen and Estrogen Metabolism;Aromatase deficiency;Sulfation Biotransformation Reaction;Metapathway biotransformation Phase I and II;Vitamin A and Carotenoid Metabolism;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules (Consensus)

Recessive Scores

• pRec: 0.576

Intolerance Scores

• loftool: 0.0652
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.36

Haploinsufficiency Scores

• pHI: 0.241
• hipred: N
• hipred_score: 0.314
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sult2b1
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: sulfate assimilation;steroid metabolic process;cholesterol metabolic process;negative regulation of cell population proliferation;positive regulation of epidermal cell differentiation;3'-phosphoadenosine 5'-phosphosulfate metabolic process
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum;cytosol;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: nucleic acid binding;alcohol sulfotransferase activity;protein binding;cholesterol binding;steroid sulfotransferase activity;steroid hormone binding