CHST5

carbohydrate sulfotransferase 5, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 16:75528530-75536108

Links

ENSG00000135702 ∙ NCBI:23563 ∙ OMIM:604817 ∙ HGNC:1973 ∙ Uniprot:Q9GZS9 ∙ 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 CHST5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST5 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						0
missense			20	6	3	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	6	3

Variants in CHST5

This is a list of pathogenic ClinVar variants found in the CHST5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-75529217-G-C		not specified	Uncertain significance (Jan 09, 2024)
16-75529268-C-T		not specified	Likely benign (Apr 12, 2022)
16-75529276-A-G		not specified	Uncertain significance (Apr 08, 2024)
16-75529339-C-A		not specified	Likely benign (Nov 23, 2022)
16-75529343-C-T		not specified	Uncertain significance (Feb 16, 2023)
16-75529421-C-G			Benign (Nov 15, 2018)
16-75529454-C-T			Benign (Nov 15, 2018)
16-75529471-T-C		not specified	Uncertain significance (Apr 08, 2024)
16-75529487-G-A		not specified	Uncertain significance (Aug 17, 2022)
16-75529562-C-A		not specified	Uncertain significance (Dec 05, 2022)
16-75529648-A-G		Rieger anomaly	Likely benign (Jan 01, 2013)
16-75529652-C-T		not specified	Uncertain significance (Dec 13, 2022)
16-75529700-C-T		not specified	Uncertain significance (Oct 20, 2021)
16-75529722-G-T		not specified	Uncertain significance (Oct 29, 2021)
16-75529745-C-T		not specified	Uncertain significance (Jun 04, 2024)
16-75529898-C-T		not specified	Uncertain significance (Oct 29, 2021)
16-75529910-C-T		not specified	Uncertain significance (Feb 23, 2023)
16-75529912-C-G		not specified	Uncertain significance (Aug 04, 2023)
16-75529936-G-T		not specified	Uncertain significance (Mar 01, 2023)
16-75529954-T-C		not specified	Uncertain significance (Aug 08, 2022)
16-75530041-C-T		not specified	Uncertain significance (Jan 10, 2022)
16-75530063-C-G		not specified	Likely benign (Apr 07, 2022)
16-75530074-T-C		not specified	Uncertain significance (Jan 04, 2024)
16-75530137-C-T		not specified	Uncertain significance (Mar 25, 2024)
16-75530207-C-T		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST5	protein_coding	protein_coding	ENST00000336257	1	6713

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000221	0.760	125639	0	66	125705	0.000263

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.351	286	303	0.943	0.0000250	2583
Missense in Polyphen		130	147.46	0.88158		1275
Synonymous	0.107	146	148	0.989	0.0000132	933
Loss of Function	1.04	7	10.7	0.657	7.24e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000704	0.000691
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000373	0.000369
Middle Eastern	0.000110	0.000109
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues and O-linked sugars of mucin-type acceptors. Acts on the non-reducing terminal GlcNAc of short carbohydrate substrates. However, it does not transfer sulfate to longer carbohydrate substrates that have poly-N-acetyllactosamine structures. Has no activity toward keratan. Not involved in generating HEV-expressed ligands for SELL. Its substrate specificity may be influenced by its subcellular location. {ECO:0000269|PubMed:10491328, ECO:0000269|PubMed:11352640, ECO:0000269|PubMed:12218059, ECO:0000269|PubMed:12626414}.
• Pathway: Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Metabolism (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.298
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• pHI: 0.0761
• hipred: N
• hipred_score: 0.238

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.235

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst5
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;N-acetylglucosamine metabolic process;protein sulfation;sulfur compound metabolic process;keratan sulfate biosynthetic process
• Cellular component: Golgi membrane;Golgi apparatus;trans-Golgi network;integral component of membrane;intrinsic component of Golgi membrane
• Molecular function: N-acetylglucosamine 6-O-sulfotransferase activity;sulfotransferase activity