ST6GALNAC3
protein-codingST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3, the group of Sialyltransferases
Gene summary
ST6GALNAC3 belongs to a family of sialyltransferases that transfer sialic acids from CMP-sialic acid to terminal positions of carbohydrate groups in glycoproteins and glycolipids (Lee et al., 1999 [PubMed 10207017]).[supplied by OMIM, Mar 2008]
- SIAT7C
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~559.9 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 ST6GALNAC3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152996.4. 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 | 42 | 1 | 43 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 44 | 1 | 0 | 45 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_694541.2 | 5 | MANE Select | |
| Ensembl | ENSP00000329214.3 | 5 | MANE Select | |
| RefSeq | NP_001153483.1 | 4 | Standard | |
| RefSeq | NP_001336034.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human)
- Globo Sphingolipid Metabolism
- Post-translational protein modification
- Metabolism of proteins
- Sialic acid metabolism
Biological Process
- ganglioside biosynthetic process
- protein glycosylation
- glycosylceramide metabolic process
- glycosphingolipid metabolic process
- glycoprotein metabolic process
Molecular Function
- alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity
- sialyltransferase activity
- (alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity
Cellular Component
- Golgi membrane
- nucleoplasm
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000328299
- Coding exons
- 5
- Length
- 559883
- Individuals with no LoFs
- 125726
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 125748
- p
- 0.0000875
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.449 | 161 | 178 | 0.905 | 0.00000952 | 2010 |
| Missense (PolyPhen) | 48 | 74.611 | 0.64333 | 843 | ||
| Synonymous | 0.275 | 61 | 63.8 | 0.956 | 0.00000359 | 568 |
| Loss of Function | 1.67 | 8 | 15.0 | 0.534 | 8.29e-7 | 175 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00035 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the biosynthesis of ganglioside GD1A from GM1B. Transfers CMP-NeuAc with an alpha-2,6-linkage to GalNAc residue on NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc of glycoproteins and glycolipids. ST6GalNAcIII prefers glycolipids to glycoproteins (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.686
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.316
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |