CHST8

carbohydrate sulfotransferase 8, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 19:33621953-33773509

Links

ENSG00000124302 ∙ NCBI:64377 ∙ OMIM:610190 ∙ HGNC:15993 ∙ Uniprot:Q9H2A9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• peeling skin syndrome type A (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Peeling skin syndrome 3	AD	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	22289416

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHST8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST8 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	3	5
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	28	4	5

Variants in CHST8

This is a list of pathogenic ClinVar variants found in the CHST8 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-33689140-C-T			Benign (May 11, 2021)
19-33689272-G-A		not specified	Uncertain significance (Feb 13, 2023)
19-33689288-G-A			Benign (Aug 01, 2022)
19-33689298-A-G		not specified	Uncertain significance (Jan 31, 2022)
19-33689299-T-C		not specified	Uncertain significance (Jan 05, 2022)
19-33771514-G-A			Benign (May 11, 2021)
19-33771960-C-A		not specified	Uncertain significance (Jan 22, 2024)
19-33771972-G-A		not specified	Likely benign (Aug 07, 2024)
19-33771979-A-G		not specified	Uncertain significance (Feb 13, 2023)
19-33772017-C-A		CHST8-related disorder	Likely benign (Aug 14, 2019)
19-33772017-C-T		Peeling skin syndrome type A • CHST8-related disorder	Conflicting classifications of pathogenicity (Dec 01, 2022)
19-33772030-G-C		not specified	Uncertain significance (Nov 12, 2024)
19-33772060-C-T		not specified	Likely benign (Feb 03, 2022)
19-33772126-G-A		not specified	Uncertain significance (Aug 04, 2024)
19-33772165-C-G		CHST8-related disorder	Likely benign (Jun 26, 2024)
19-33772177-C-T		not specified	Uncertain significance (Jan 24, 2024)
19-33772203-C-T		not specified	Uncertain significance (Nov 30, 2022)
19-33772205-C-A		CHST8-related disorder	Likely benign (Jan 31, 2024)
19-33772207-G-C		not specified	Uncertain significance (Sep 30, 2024)
19-33772230-A-G		not specified	Uncertain significance (Dec 07, 2023)
19-33772240-G-A		not specified	Likely benign (Nov 21, 2024)
19-33772254-C-A		not specified	Uncertain significance (Dec 13, 2023)
19-33772266-A-G		not specified	Uncertain significance (Jul 27, 2024)
19-33772291-G-C		not specified	Uncertain significance (Jul 06, 2021)
19-33772295-G-GAGC		CHST8-related disorder	Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST8	protein_coding	protein_coding	ENST00000262622	3	151554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000108	0.831	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	266	316	0.840	0.0000239	2726
Missense in Polyphen		80	110.52	0.72387		939
Synonymous	0.967	125	140	0.896	0.0000105	900
Loss of Function	1.26	8	12.9	0.620	7.23e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000400	0.000397
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000580	0.0000544
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000988	0.0000967
Middle Eastern	0.0000580	0.0000544
South Asian	0.000174	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of sulfate to position 4 of non- reducing N-acetylgalactosamine (GalNAc) residues in both N-glycans and O-glycans. Required for biosynthesis of glycoprotein hormones lutropin and thyrotropin, by mediating sulfation of their carbohydrate structures. Only active against terminal GalNAcbeta1,GalNAcbeta. Not active toward chondroitin. {ECO:0000269|PubMed:10988300, ECO:0000269|PubMed:11445554}.
• Disease: DISEASE: Peeling skin syndrome 3 (PSS3) [MIM:616265]: A form of peeling skin syndrome, a genodermatosis characterized by generalized, continuous shedding of the outer layers of the epidermis. Two main PSS subtypes have been suggested. Patients with non-inflammatory PSS (type A) manifest white scaling, with painless and easy removal of the skin, irritation when in contact with water, dust and sand, and no history of erythema, pruritis or atopy. Inflammatory PSS (type B) is associated with generalized erythema, pruritus and atopy. It is an ichthyosiform erythroderma characterized by lifelong patchy peeling of the entire skin with onset at birth or shortly after. Several patients have been reported with high IgE levels. PSS3 is characterized by generalized white scaling occurring over the upper and lower extremities. Symptoms start during the second half of the first decade of life. {ECO:0000269|PubMed:22289416}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Metapathway biotransformation Phase I and II;Post-translational protein modification;Reactions specific to the complex N-glycan synthesis pathway;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.629
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.886
• hipred: N
• hipred_score: 0.478
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.563

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst8
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; vision/eye phenotype

Gene ontology

• Biological process: sulfur compound metabolic process;central nervous system development;carbohydrate biosynthetic process;proteoglycan biosynthetic process;hormone biosynthetic process
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: N-acetylgalactosamine 4-O-sulfotransferase activity