ST6GALNAC2
protein-codingST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 2, the group of Sialyltransferases
Gene summary
ST6GALNAC2 belongs to a family of sialyltransferases that add sialic acids to the nonreducing ends of glycoconjugates. At the cell surface, these modifications have roles in cell-cell and cell-substrate interactions, bacterial adhesion, and protein targeting (Samyn-Petit et al., 2000 [PubMed 10742600]).[supplied by OMIM, Mar 2008]
- SIAT7
- SIAT7B
- SIATL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.6 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 ST6GALNAC2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006456.3. 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 | 2 | 2 | ||||
| missense | 65 | 3 | 68 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 68 | 3 | 0 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006447.2 | 9 | MANE Select | |
| Ensembl | ENSP00000225276.4 | 9 | MANE Select | |
| Ensembl | ENSP00000464915.1 | 2 | Standard | |
| Ensembl | ENSP00000466513.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Globo Sphingolipid Metabolism
- Post-translational protein modification
- Metabolism of proteins
- Sialic acid metabolism
- Synthesis of substrates in N-glycan biosythesis
Biological Process
- protein glycosylation
- protein O-linked glycosylation
- O-glycan processing
- protein sialylation
Molecular Function
- alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity
- sialyltransferase activity
Cellular Component
- Golgi membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000225276
- Coding exons
- 9
- Length
- 23247
- Individuals with no LoFs
- 125659
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 88
- Defined
- 125748
- p
- 0.000354
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.242 | 205 | 215 | 0.954 | 0.0000127 | 2400 |
| Missense (PolyPhen) | 79 | 90.716 | 0.87085 | 988 | ||
| Synonymous | -0.881 | 107 | 96.0 | 1.11 | 0.00000606 | 768 |
| Loss of Function | -0.640 | 20 | 17.1 | 1.17 | 8.10e-7 | 199 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00049 | 0.00049 | rare |
| Latino/Admixed American | 0.00044 | 0.00043 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00055 | 0.00050 | rare |
| South Asian | 0.00020 | 0.00016 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the transfer of N-acetylneuraminyl groups onto glycan chains in glycoproteins. {ECO:0000269|PubMed:10742600, ECO:0000269|PubMed:29251719}.;
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- LoFtool
- 0.759
- RVIS EVS
- 0.0000761
- RVIS percentile EVS
- 53.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.483
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |