GALNT1
polypeptide N-acetylgalactosaminyltransferase 1, the group of MicroRNA protein coding host genes|Polypeptide N-acetylgalactosaminyltransferases
Basic information
Region (hg38): 18:35581117-35711834
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT1 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 1 |
Variants in GALNT1
This is a list of pathogenic ClinVar variants found in the GALNT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-35663637-C-T | not specified | Uncertain significance (Oct 18, 2021) | ||
| 18-35663644-A-C | not specified | Uncertain significance (Jan 11, 2023) | ||
| 18-35683406-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
| 18-35683466-G-A | not specified | Uncertain significance (Nov 15, 2024) | ||
| 18-35687137-C-G | not specified | Uncertain significance (Mar 29, 2022) | ||
| 18-35691091-C-T | not specified | Uncertain significance (Mar 28, 2023) | ||
| 18-35691169-A-G | not specified | Uncertain significance (Jan 17, 2023) | ||
| 18-35691180-A-G | not specified | Uncertain significance (Nov 25, 2024) | ||
| 18-35692220-T-C | not specified | Uncertain significance (Sep 07, 2022) | ||
| 18-35692298-G-A | not specified | Uncertain significance (May 20, 2024) | ||
| 18-35702978-G-A | not specified | Uncertain significance (Jul 30, 2024) | ||
| 18-35703550-C-T | Benign (Dec 31, 2019) | |||
| 18-35709663-G-C | not specified | Uncertain significance (Dec 02, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GALNT1 | protein_coding | protein_coding | ENST00000269195 | 11 | 130718 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00191 | 0.998 | 125727 | 1 | 14 | 125742 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.52 | 174 | 296 | 0.588 | 0.0000146 | 3701 |
| Missense in Polyphen | 29 | 96.374 | 0.30091 | 1191 | ||
| Synonymous | 1.15 | 84 | 98.5 | 0.852 | 0.00000475 | 1026 |
| Loss of Function | 3.26 | 10 | 28.9 | 0.346 | 0.00000156 | 347 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000304 | 0.0000304 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000895 | 0.0000879 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.000172 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D- galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b and Muc7. {ECO:0000269|PubMed:9295285}.;
- 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;Metabolism of Spingolipids in ER and Golgi apparatus;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;O-linked glycosylation of mucins;O-linked glycosylation;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.408
- rvis_EVS
- -0.41
- rvis_percentile_EVS
- 26.23
Haploinsufficiency Scores
- pHI
- 0.454
- hipred
- Y
- hipred_score
- 0.792
- ghis
- 0.662
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.333
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Galnt1
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- protein O-linked glycosylation;O-glycan processing;protein O-linked glycosylation via serine;protein O-linked glycosylation via threonine
- Cellular component
- Golgi membrane;extracellular region;endoplasmic reticulum membrane;Golgi apparatus;membrane;integral component of membrane;Golgi cisterna membrane;perinuclear region of cytoplasm
- Molecular function
- polypeptide N-acetylgalactosaminyltransferase activity;manganese ion binding;carbohydrate binding