CHST14

carbohydrate sulfotransferase 14, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 15:40470984-40473158

Previous symbols: [ "D4ST1" ]

Links

ENSG00000169105 ∙ NCBI:113189 ∙ OMIM:608429 ∙ HGNC:24464 ∙ Uniprot:Q8NCH0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Ehlers-Danlos syndrome, musculocontractural type (Supportive), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 1 (Definitive), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 1 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 1 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 1 (Definitive), mode of inheritance: AR
• Ehlers-Danlos syndrome, musculocontractural type 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ehlers-Danlos syndrome, musculocontractural type 1	AR	Hematologic; Musculoskeletal; Ophthalmologic	Clinical issues relate to connective tissue fragility may affect multiple organs, and may include severe bleeding episodes (eg, after minor trauma), such that recognition may allow precautions and preventive measures, as well as rapid treatment in the case of bleeding; Medical treatment (eg, with oral dermatan sulfate) may be beneficial; Due to risk of glaucoma, surveillance may allow early management	Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dermatologic; Gastrointestinal; Hematologic; Musculoskeletal; Ophthalmologic	9084938; 10766984; 11370633; 16158441; 20004762; 20503305; 20842734; 20533528; 21744491; 22581468; 22407744; 22987394; 23704329

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHST14 gene.

• Ehlers-Danlos syndrome, musculocontractural type (9 variants)
• Ehlers-Danlos syndrome, musculocontractural type 1 (3 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST14 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	90		92
missense	1	3	149	3		156
nonsense	5					5
start loss						0
frameshift	7	4	2			13
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				4	1	5
Total	13	7	153	97	1

Highest pathogenic variant AF is 0.00000658

Variants in CHST14

This is a list of pathogenic ClinVar variants found in the CHST14 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-40471029-C-T			Likely benign (May 19, 2019)
15-40471187-C-G		not specified	Likely benign (Aug 18, 2017)
15-40471209-G-A		not specified	Likely benign (Nov 04, 2016)
15-40471215-T-C		Ehlers-Danlos syndrome, musculocontractural type	Conflicting classifications of pathogenicity (Oct 02, 2023)
15-40471221-C-T		Ehlers-Danlos syndrome, musculocontractural type • Cardiovascular phenotype	Uncertain significance (Jun 27, 2022)
15-40471223-C-T		Cardiovascular phenotype	Uncertain significance (Jan 25, 2023)
15-40471224-G-C		Ehlers-Danlos syndrome, musculocontractural type • Cardiovascular phenotype	Uncertain significance (Nov 21, 2023)
15-40471231-G-T		Ehlers-Danlos syndrome, musculocontractural type	Likely benign (Jan 20, 2024)
15-40471233-C-A		Ehlers-Danlos syndrome, musculocontractural type • Ehlers-Danlos syndrome, musculocontractural type 1	Uncertain significance (Oct 04, 2022)
15-40471236-C-T		Cardiovascular phenotype	Uncertain significance (Oct 21, 2022)
15-40471242-C-T		Cardiovascular phenotype	Uncertain significance (Mar 19, 2024)
15-40471245-C-T		Ehlers-Danlos syndrome, musculocontractural type	Uncertain significance (Aug 09, 2022)
15-40471247-C-T		Cardiovascular phenotype	Uncertain significance (Sep 09, 2021)
15-40471250-A-G		Cardiovascular phenotype	Uncertain significance (Aug 27, 2020)
15-40471256-G-C		Ehlers-Danlos syndrome, musculocontractural type • Cardiovascular phenotype	Uncertain significance (Mar 22, 2021)
15-40471256-G-T		Cardiovascular phenotype	Uncertain significance (Aug 07, 2022)
15-40471258-C-G		Ehlers-Danlos syndrome, musculocontractural type	Likely benign (Feb 05, 2020)
15-40471259-G-A			Uncertain significance (Jan 17, 2020)
15-40471261-G-A		Cardiovascular phenotype • Ehlers-Danlos syndrome, musculocontractural type	Likely benign (Jun 14, 2022)
15-40471261-G-T		Cardiovascular phenotype	Uncertain significance (Mar 15, 2024)
15-40471262-C-T		Cardiovascular phenotype	Uncertain significance (Aug 03, 2022)
15-40471271-C-T		Ehlers-Danlos syndrome, musculocontractural type • Cardiovascular phenotype	Likely benign (Sep 10, 2023)
15-40471272-G-C		Cardiovascular phenotype	Uncertain significance (May 24, 2021)
15-40471274-G-A		Ehlers-Danlos syndrome, musculocontractural type 1	Uncertain significance (Jan 24, 2018)
15-40471274-G-T		Cardiovascular phenotype	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST14	protein_coding	protein_coding	ENST00000306243	1	2194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.447	0.547	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.683	182	210	0.867	0.0000108	2370
Missense in Polyphen		57	66.339	0.85922		844
Synonymous	0.703	87	95.8	0.909	0.00000479	841
Loss of Function	2.31	2	9.83	0.203	5.21e-7	98

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of dermatan sulfate. Plays a pivotal role in the formation of 4-0-sulfated IdoA blocks in dermatan sulfate. Transfers sulfate to the C-4 hydroxyl of beta1,4-linked GalNAc that is substituted with an alpha-linked iduronic acid (IdoUA) at the C-3 hydroxyl. Transfers sulfate more efficiently to GalNAc residues in -IdoUA-GalNAc-IdoUA- than in -GlcUA-GalNAc-GlcUA-sequences. Has preference for partially desulfated dermatan sulfate. Addition of sulfate to GalNAc may occur immediately after epimerization of GlcUA to IdoUA. Appears to have an important role in the formation of the cerebellar neural network during postnatal brain development. {ECO:0000269|PubMed:19661164}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metapathway biotransformation Phase I and II;Metabolism of carbohydrates;Dermatan sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;dermatan sulfate biosynthesis (late stages);dermatan sulfate biosynthesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.574
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.313
• hipred: Y
• hipred_score: 0.516
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chst14
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; craniofacial 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: carbohydrate biosynthetic process;dermatan sulfate biosynthetic process;dermatan sulfate proteoglycan metabolic process
• Cellular component: Golgi membrane;integral component of membrane;extracellular exosome
• Molecular function: N-acetylgalactosamine 4-O-sulfotransferase activity;phosphate ion binding