CSGALNACT2
protein-codingchondroitin sulfate N-acetylgalactosaminyltransferase 2, the group of Beta 4-glycosyltransferases
Gene summary
This gene encodes a member of the chondroitin N-acetylgalactosaminyltransferase family. The encoded protein is involved in elongation during chondroitin sulfate synthesis. Alternative splicing of this gene results in multiple transcript variants. Two related pseudogenes have been identified on chromosome X. [provided by RefSeq, Feb 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~46.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CSGALNACT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018590.5. 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 | 0 | |||||
| missense | 79 | 4 | 83 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 81 | 4 | 0 | 85 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061060.3 | 7 | MANE Select | |
| Ensembl | ENSP00000363590.3 | 7 | MANE Select | |
| RefSeq | NP_001306583.1 | 6 | Standard | |
| RefSeq | NP_001306585.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human)
- Metabolism of carbohydrates
- Chondroitin sulfate biosynthesis
- Chondroitin sulfate/dermatan sulfate metabolism
- Glycosaminoglycan metabolism
Biological Process
- proteoglycan biosynthetic process
- chondroitin sulfate biosynthetic process
- chondroitin sulfate proteoglycan biosynthetic process
- dermatan sulfate proteoglycan biosynthetic process
- dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process
Molecular Function
- protein binding
- acetylgalactosaminyltransferase activity
- metal ion binding
- glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity
- glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity
Cellular Component
- Golgi membrane
- membrane
- integral component of Golgi membrane
- Golgi cisterna membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000374466
- Coding exons
- 7
- Length
- 46823
- Individuals with no LoFs
- 125732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125748
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.12 | 243 | 297 | 0.817 | 0.0000155 | 3590 |
| Missense (PolyPhen) | 92 | 118.06 | 0.77924 | 1511 | ||
| Synonymous | 0.120 | 101 | 103 | 0.985 | 0.00000504 | 998 |
| Loss of Function | 3.51 | 6 | 24.9 | 0.241 | 0.00000139 | 296 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000088 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000088 | 0.000088 | rare |
| South Asian | 0.000067 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP- GalNAc to the non-reducing end of glucuronic acid (GlcUA). Required for addition of the first GalNAc to the core tetrasaccharide linker and for elongation of chondroitin chains. {ECO:0000269|PubMed:12433924, ECO:0000269|PubMed:12446672}.;
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- LoFtool
- 0.703
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 34.71
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.289
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |