GALNT7
Basic information
Region (hg38): 4:173168811-173323967
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (55 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017423.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 54 | 55 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 54 | 1 | 2 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GALNT7 | protein_coding | protein_coding | ENST00000265000 | 12 | 155215 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000259 | 1.00 | 125704 | 0 | 44 | 125748 | 0.000175 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.79 | 266 | 362 | 0.735 | 0.0000182 | 4326 |
Missense in Polyphen | 83 | 133.61 | 0.62121 | 1544 | ||
Synonymous | 1.80 | 101 | 127 | 0.796 | 0.00000655 | 1208 |
Loss of Function | 3.28 | 16 | 37.7 | 0.424 | 0.00000207 | 430 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000327 | 0.000326 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000117 | 0.000109 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.000207 | 0.000202 |
Middle Eastern | 0.000117 | 0.000109 |
South Asian | 0.000229 | 0.000229 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Glycopeptide transferase involved in O-linked oligosaccharide biosynthesis, which catalyzes the transfer of an N-acetyl-D-galactosamine residue to an already glycosylated peptide. In contrast to other proteins of the family, it does not act as a peptide transferase that transfers GalNAc onto serine or threonine residue on the protein receptor, but instead requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. Some peptide transferase activity is however not excluded, considering that its appropriate peptide substrate may remain unidentified.;
- Pathway
- Mucin type O-glycan biosynthesis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.856
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.85
Haploinsufficiency Scores
- pHI
- 0.242
- hipred
- Y
- hipred_score
- 0.639
- ghis
- 0.466
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.236
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Galnt7
- Phenotype
Gene ontology
- Biological process
- carbohydrate metabolic process;protein O-linked glycosylation;O-glycan processing
- Cellular component
- Golgi membrane;Golgi apparatus;membrane;integral component of membrane;extracellular exosome
- Molecular function
- polypeptide N-acetylgalactosaminyltransferase activity;carbohydrate binding;metal ion binding