POMGNT2
protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-), the group of O-linked N-acetylglucosaminyltransferases
Basic information
Region (hg38): 3:43079229-43106085
Previous symbols: [ "C3orf39", "GTDC2" ]
Links
Phenotypes
GenCC
Source:
- muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 (Strong), mode of inheritance: AR
- muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 (Moderate), mode of inheritance: AR
- muscular dystrophy-dystroglycanopathy, type A (Supportive), mode of inheritance: AR
- muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 (Definitive), mode of inheritance: AR
- muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 (Strong), mode of inheritance: AR
- myopathy caused by variation in POMGNT2 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 8; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal; Neurologic; Ophthalmologic | 22958903; 27066570 |
ClinVar
This is a list of variants' phenotypes submitted to
- Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 (14 variants)
- Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the POMGNT2 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 133 | 137 | ||||
| missense | 241 | 250 | ||||
| nonsense | 9 | |||||
| start loss | 0 | |||||
| frameshift | 13 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 14 | 8 | 244 | 140 | 3 |
Highest pathogenic variant AF is 0.00000657203
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| POMGNT2 | protein_coding | protein_coding | ENST00000344697 | 1 | 26845 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000556 | 0.884 | 125719 | 0 | 29 | 125748 | 0.000115 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.955 | 323 | 375 | 0.861 | 0.0000253 | 3755 |
| Missense in Polyphen | 130 | 159.25 | 0.81633 | 1738 | ||
| Synonymous | -0.387 | 169 | 163 | 1.04 | 0.0000106 | 1265 |
| Loss of Function | 1.53 | 11 | 18.0 | 0.610 | 0.00000104 | 165 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000187 | 0.000185 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: O-linked mannose beta-1,4-N- acetylglucosaminyltransferase that transfers UDP-N-acetyl-D- glucosamine to the 4-position of the mannose to generate N-acetyl- D-glucosamine-beta-1,4-O-D-mannosylprotein. Involved in the biosynthesis of the phosphorylated O-mannosyl trisaccharide (N- acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate- 6-)mannose), a carbohydrate structure present in alpha- dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity. {ECO:0000269|PubMed:23929950}.;
- Pathway
- Mannose type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-linked glycosylation
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.88
- rvis_percentile_EVS
- 10.54
Haploinsufficiency Scores
- pHI
- 0.218
- hipred
- N
- hipred_score
- 0.304
- ghis
- 0.560
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pomgnt2
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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);
Zebrafish Information Network
- Gene name
- pomgnt2
- Affected structure
- muscle
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- neuron migration;protein O-linked glycosylation;protein O-linked mannosylation
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
- Molecular function
- protein binding;acetylglucosaminyltransferase activity;protein O-GlcNAc transferase activity