CHST11

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the sulfotransferase 2 family. It is localized to the golgi membrane, and 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. A chromosomal translocation involving this gene and IgH, t(12;14)(q23;q32), has been reported in a patient with B-cell chronic lymphocytic leukemia. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

MANE transcript

NM_018413.6

Inheritance

ClinVar variants

U:39B:10

Top phenotype

Osteochondrodysplasia, brachydactyly, and overlapping malformed digits

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr12:104,455,295-104,762,014

External References & Databases

Ensembl (ENSG00000171310)

Transcript & Mutation Effects

hg38 • Region Span ~306.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

osteochondrodysplasia, brachydactyly, and overlapping malformed digitsLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0032574

Submitter: Ambry Genetics

congenital disorder of glycosylationLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0015286

Submitter: ClinGen

*CHST11* was first reported in relation to congenital disorder of glycosylation (also known as osteochondrodysplasia, brachydactyly, and overlapping malformed digits) in 2015 (Chopra et al., PMID: 26436107). Two variants (gross deletion, inframe deletion) that have been reported in two probands in two publications are included in this curation. This gene-disease relationship is also supported by segregation evidence (Shabbir et al., PMID: 29514872), biochemical function studies (Hiraoka, et al., PMID: 10781601), and a mouse model (Klüppel et al., PMID: 16079159). In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen Congenital Disorders of Glycosylation GCEP on the meeting date October 5, 2026 (SOP Version 12).

osteochondrodysplasia, brachydactyly, and overlapping malformed digitsSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032574

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Osteochondrodysplasia, brachydactyly, and overlapping malformed digitsAR

Manifestation: Musculoskeletal

Intervention: General

Rationale: 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

Refs: 26436107; 29514872

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHST11 variants in ClinVar

9 Conditions Cataloged

not specifiedTotal: 45

CHST11-related disorderTotal: 5

Osteochondrodysplasia, brachydactyly, and overlapping malformed digitsTotal: 2

not providedTotal: 1

Synpolydactyly type 1Total: 1

clino-symphalangismTotal: 1

ChondrodysplasiaTotal: 1

overriding digitsTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018413.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	6 clinvar		7
missense			38 clinvar	4 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	10	0	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018413.6	RefSeq	NP_060883.1	3	MANE Select
ENST00000303694.6	Ensembl	ENSP00000305725.5	3	MANE Select
NM_001173982.2	RefSeq	NP_001167453.1	3	Standard
ENST00000546689.1	Ensembl	ENSP00000448678.1	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
chst11	Danio rerio	Structure: motor neuron Quality: branchiness abnormal

Gene / Model

Organism

Observed Phenotype

chst11

Danio rerio

Structure: motor neuron

Quality: branchiness

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human)
Sulfate/Sulfite Metabolism
Sulfite oxidase deficiency
Spinal Cord Injury
Endochondral Ossification

Biological Process

chondrocyte development
respiratory gaseous exchange
post-embryonic development
carbohydrate biosynthetic process
chondroitin sulfate biosynthetic process

Molecular Function

N-acetylgalactosamine 4-O-sulfotransferase activity
chondroitin 4-sulfotransferase activity
N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity

Cellular Component

Golgi membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000303694
Coding exons: 3
Length: 306720
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.84	146	223	0.654	0.0000147	2322
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.149

Intolerance Scores

LoFtool: 0.314
RVIS EVS: -0.38
RVIS percentile EVS: 27.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.830

Gene Damage Prediction

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