ST6GALNAC1
protein-codingST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1, the group of Sialyltransferases
Gene summary
Glycosylation of proteins affects cell-cell interaction, interactions with the matrix, and the functions of intracellular molecules. ST6GALNAC1 transfers a sialic acid, N-acetylneuraminic acid (NeuAc), in an alpha-2,6 linkage to O-linked GalNAc residues. The cancer-associated sialyl-Tn (sTn) antigen is formed by ST6GALNAC1-catalyzed sialylation of GalNAc residues on mucins (Ikehara et al., 1999 [PubMed 10536037]; Sewell et al., 2006 [PubMed 16319059]).[supplied by OMIM, Mar 2008]
- SIAT7A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~19.0 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 ST6GALNAC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018414.5. 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 | 2 | 2 | ||||
| missense | 76 | 8 | 1 | 85 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 80 | 8 | 1 | 89 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060884.1 | 9 | MANE Select | |
| Ensembl | ENSP00000156626.6 | 9 | MANE Select | |
| RefSeq | NP_001276036.1 | 8 | Standard | |
| Ensembl | ENSP00000351991.4 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mucin type O-glycan biosynthesis - Homo sapiens (human)
- Globo Sphingolipid Metabolism
- Post-translational protein modification
- Metabolism of proteins
- O-Glycan biosynthesis
Biological Process
- protein glycosylation
- oligosaccharide biosynthetic process
- 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
- ENST00000156626
- Coding exons
- 9
- Length
- 19078
- Individuals with no LoFs
- 125610
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 138
- Defined
- 125748
- p
- 0.000549
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.141 | 341 | 348 | 0.979 | 0.0000207 | 3907 |
| Missense (PolyPhen) | 97 | 106.22 | 0.91322 | 1204 | ||
| Synonymous | 0.0390 | 141 | 142 | 0.996 | 0.00000879 | 1204 |
| Loss of Function | 1.06 | 20 | 25.8 | 0.774 | 0.00000128 | 282 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00050 | 0.00049 | rare |
| Latino/Admixed American | 0.0011 | 0.00095 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.00055 | 0.00055 | rare |
| European (Non-Finnish) | 0.00054 | 0.00052 | rare |
| South Asian | 0.00060 | 0.00059 | rare |
| Other | 0.00039 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- LoFtool
- 0.967
- RVIS EVS
- 0.16
- RVIS percentile EVS
- 64.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.350
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |