GNPDA1
glucosamine-6-phosphate deaminase 1
Basic information
Region (hg38): 5:141991748-142013041
Previous symbols: [ "GNPI" ]
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 GNPDA1 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 | 0 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in GNPDA1
This is a list of pathogenic ClinVar variants found in the GNPDA1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-142003157-G-A | not specified | Uncertain significance (Oct 22, 2021) | ||
| 5-142003210-A-G | not specified | Uncertain significance (Jun 21, 2022) | ||
| 5-142003244-C-G | not specified | Uncertain significance (Mar 04, 2024) | ||
| 5-142004946-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 5-142004963-A-G | not specified | Uncertain significance (Apr 07, 2022) | ||
| 5-142005065-A-T | not specified | Uncertain significance (Feb 06, 2024) | ||
| 5-142006224-T-G | not specified | Uncertain significance (Nov 29, 2023) | ||
| 5-142006233-A-G | not specified | Uncertain significance (Sep 17, 2021) | ||
| 5-142006242-G-A | not specified | Uncertain significance (Feb 27, 2023) | ||
| 5-142006264-T-C | not specified | Uncertain significance (Jun 29, 2023) | ||
| 5-142006287-A-G | not specified | Uncertain significance (Aug 01, 2023) | ||
| 5-142006308-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 5-142011959-T-C | not specified | Uncertain significance (Jun 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GNPDA1 | protein_coding | protein_coding | ENST00000508177 | 6 | 21293 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.60e-7 | 0.237 | 125718 | 0 | 30 | 125748 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.79 | 104 | 169 | 0.614 | 0.00000916 | 1929 |
| Missense in Polyphen | 35 | 67.278 | 0.52023 | 776 | ||
| Synonymous | -0.545 | 75 | 69.2 | 1.08 | 0.00000446 | 528 |
| Loss of Function | 0.284 | 11 | 12.1 | 0.912 | 5.74e-7 | 149 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000360 | 0.000360 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000160 | 0.000158 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Seems to trigger calcium oscillations in mammalian eggs. These oscillations serve as the essential trigger for egg activation and early development of the embryo (By similarity). {ECO:0000250}.;
- Pathway
- UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II;Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;<i>N</i>-acetylglucosamine degradation II;Aminosugars metabolism;Metabolism of carbohydrates;Fructose Mannose metabolism;<i>N</i>-acetylglucosamine degradation I;Metabolism;Glycolysis;Glucose metabolism
(Consensus)
Recessive Scores
- pRec
- 0.164
Intolerance Scores
- loftool
- 0.637
- rvis_EVS
- -0.47
- rvis_percentile_EVS
- 23.04
Haploinsufficiency Scores
- pHI
- 0.255
- hipred
- Y
- hipred_score
- 0.528
- ghis
- 0.587
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.981
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gnpda1
- 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); embryo phenotype; renal/urinary system 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); growth/size/body region phenotype;
Gene ontology
- Biological process
- carbohydrate metabolic process;glucosamine catabolic process;N-acetylglucosamine catabolic process;UDP-N-acetylglucosamine biosynthetic process;generation of precursor metabolites and energy;single fertilization;N-acetylneuraminate catabolic process
- Cellular component
- cytoplasm;cytosol;extracellular exosome
- Molecular function
- glucosamine-6-phosphate deaminase activity;protein binding;identical protein binding