CHST12

carbohydrate sulfotransferase 12, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 7:2403588-2448484

Links

ENSG00000136213 ∙ NCBI:55501 ∙ OMIM:610129 ∙ HGNC:17423 ∙ Uniprot:Q9NRB3 ∙ 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 CHST12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST12 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			35	1	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	2	1

Variants in CHST12

This is a list of pathogenic ClinVar variants found in the CHST12 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-2432644-C-T		not specified	Uncertain significance (Apr 23, 2024)
7-2432676-C-G		not specified	Uncertain significance (Nov 03, 2022)
7-2432732-C-T			Likely benign (Jul 23, 2018)
7-2432779-C-T		not specified	Uncertain significance (Apr 23, 2024)
7-2432800-C-T		not specified	Uncertain significance (Jun 28, 2023)
7-2432808-G-T		not specified	Uncertain significance (Jul 17, 2023)
7-2432821-C-G		not specified	Uncertain significance (Jan 04, 2024)
7-2432834-T-G		not specified	Uncertain significance (May 16, 2023)
7-2432836-T-A		not specified	Uncertain significance (Feb 10, 2022)
7-2432854-A-G		not specified	Uncertain significance (May 28, 2024)
7-2432855-G-C		not specified	Uncertain significance (Dec 05, 2022)
7-2432883-G-A		not specified	Uncertain significance (Nov 17, 2023)
7-2432902-C-T		not specified	Uncertain significance (Apr 18, 2023)
7-2432928-A-G		not specified	Uncertain significance (May 02, 2024)
7-2432938-G-C		not specified	Uncertain significance (Nov 12, 2021)
7-2432962-C-T		not specified	Uncertain significance (Oct 05, 2023)
7-2432973-C-T		not specified	Uncertain significance (May 20, 2024)
7-2433058-C-T		not specified	Uncertain significance (Sep 06, 2022)
7-2433181-T-A		not specified	Uncertain significance (Apr 26, 2023)
7-2433223-C-G		not specified	Uncertain significance (Nov 05, 2021)
7-2433228-C-T		not specified	Uncertain significance (Feb 27, 2024)
7-2433240-C-T		not specified	Uncertain significance (Apr 28, 2022)
7-2433247-C-T		not specified	Uncertain significance (Apr 21, 2022)
7-2433250-G-A		not specified	Uncertain significance (Sep 07, 2022)
7-2433252-G-A		not specified	Uncertain significance (Apr 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST12	protein_coding	protein_coding	ENST00000258711	1	31020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000466	0.667	125670	0	27	125697	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.148	306	313	0.977	0.0000261	2692
Missense in Polyphen		95	119.97	0.79186		1153
Synonymous	-1.84	178	149	1.19	0.0000138	846
Loss of Function	0.895	8	11.2	0.712	4.89e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000951	0.0000924
European (Non-Finnish)	0.000151	0.000150
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin and desulfated dermatan sulfate. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Activity toward partially desulfated dermatan sulfate is however lower. Does not form 4, 6-di-O-sulfated GalNAc when chondroitin sulfate C is used as an acceptor.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;chondroitin sulfate biosynthesis (late stages);Proteoglycan biosynthesis;chondroitin sulfate biosynthesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.412
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.58

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.379
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst12

Gene ontology

• Biological process: carbohydrate biosynthetic process;chondroitin sulfate biosynthetic process;dermatan sulfate biosynthetic process
• Cellular component: Golgi membrane;membrane;integral component of Golgi membrane
• Molecular function: chondroitin 4-sulfotransferase activity;3'-phosphoadenosine 5'-phosphosulfate binding