CHST11

carbohydrate sulfotransferase 11, the group of Sulfotransferases, membrane bound|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:104455295-104762014

Links

ENSG00000171310 ∙ NCBI:50515 ∙ OMIM:610128 ∙ HGNC:17422 ∙ Uniprot:Q9NPF2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• osteochondrodysplasia, brachydactyly, and overlapping malformed digits (Limited), mode of inheritance: AR
• osteochondrodysplasia, brachydactyly, and overlapping malformed digits (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Osteochondrodysplasia, brachydactyly, and overlapping malformed digits	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	Musculoskeletal	26436107; 29514872

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHST11 gene.

• not_specified (40 variants)
• CHST11-related_disorder (4 variants)
• Osteochondrodysplasia,_brachydactyly,_and_overlapping_malformed_digits (2 variants)
• not_provided (1 variants)
• Synpolydactyly_type_1 (1 variants)
• clino-symphalangism (1 variants)
• Chondrodysplasia (1 variants)
• overriding_digits (1 variants)
• Brachydactyly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHST11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018413.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	2		3
missense			38	3		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	5	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHST11	protein_coding	protein_coding	ENST00000303694	3	306720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.84	146	223	0.654	0.0000147	2322
Missense in Polyphen		44	87.019	0.50564		838
Synonymous	0.835	84	94.3	0.891	0.00000664	675
Loss of Function	2.69	3	13.8	0.218	7.61e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000626	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000544	0.0000544
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 chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Can also sulfate Gal residues in desulfated dermatan sulfate. Preferentially sulfates in GlcA->GalNAc unit than in IdoA->GalNAc unit. Does not form 4, 6- di-O-sulfated GalNAc when chondroitin sulfate C is used as an acceptor.
• Disease: DISEASE: Note=A chromosomal aberration involving CHST11 is found in B-cell chronic lymphocytic leukemias. Translocation t(12;14)(q23;q32) with IgH. {ECO:0000269|PubMed:15273723}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Sulfate/Sulfite Metabolism;Sulfite oxidase deficiency;Spinal Cord Injury;Endochondral Ossification;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: 0.149

Intolerance Scores

• loftool: 0.314
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.830

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: chst11
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: branchiness

Gene ontology

• Biological process: chondrocyte development;respiratory gaseous exchange;post-embryonic development;carbohydrate biosynthetic process;chondroitin sulfate biosynthetic process;negative regulation of transforming growth factor beta receptor signaling pathway;polysaccharide localization;post-anal tail morphogenesis;regulation of cell population proliferation;embryonic digit morphogenesis;negative regulation of apoptotic process;developmental growth;embryonic viscerocranium morphogenesis
• Cellular component: Golgi membrane;membrane;integral component of membrane
• Molecular function: N-acetylgalactosamine 4-O-sulfotransferase activity;chondroitin 4-sulfotransferase activity;N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity