GAPDH
glyceraldehyde-3-phosphate dehydrogenase
Basic information
Region (hg38): 12:6534512-6538374
Previous symbols: [ "GAPD" ]
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 GAPDH 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 5 | 0 | 1 |
Variants in GAPDH
This is a list of pathogenic ClinVar variants found in the GAPDH region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-6534825-C-G | Benign (Aug 22, 2019) | |||
| 12-6536494-A-T | not specified | Likely benign (Aug 21, 2024) | ||
| 12-6537127-G-T | not specified | Uncertain significance (Dec 14, 2023) | ||
| 12-6537128-G-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 12-6537359-A-G | not specified | Uncertain significance (Apr 20, 2023) | ||
| 12-6537813-C-G | not specified | Uncertain significance (Jan 16, 2024) | ||
| 12-6538130-G-A | not specified | Uncertain significance (Sep 06, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GAPDH | protein_coding | protein_coding | ENST00000229239 | 8 | 4445 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.114 | 0.881 | 125721 | 0 | 27 | 125748 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.81 | 130 | 203 | 0.642 | 0.0000112 | 2215 |
| Missense in Polyphen | 19 | 30.567 | 0.62159 | 454 | ||
| Synonymous | -3.60 | 120 | 79.3 | 1.51 | 0.00000483 | 661 |
| Loss of Function | 2.43 | 4 | 13.7 | 0.292 | 6.71e-7 | 163 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000425 | 0.000423 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000882 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000229 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has both glyceraldehyde-3-phosphate dehydrogenase and nitrosylase activities, thereby playing a role in glycolysis and nuclear functions, respectively. Participates in nuclear events including transcription, RNA transport, DNA replication and apoptosis. Nuclear functions are probably due to the nitrosylase activity that mediates cysteine S-nitrosylation of nuclear target proteins such as SIRT1, HDAC2 and PRKDC. Modulates the organization and assembly of the cytoskeleton. Facilitates the CHP1-dependent microtubule and membrane associations through its ability to stimulate the binding of CHP1 to microtubules (By similarity). Glyceraldehyde-3-phosphate dehydrogenase is a key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D- glyceroyl phosphate. Component of the GAIT (gamma interferon- activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma treatment assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation. {ECO:0000250, ECO:0000269|PubMed:11724794, ECO:0000269|PubMed:23071094, ECO:0000269|PubMed:3170585}.;
- Pathway
- Glycolysis / Gluconeogenesis - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Warburg Effect;Mitochondrial Electron Transport Chain;Glycolysis;Glycogenosis, Type VII. Tarui disease;Gluconeogenesis;Glycerol Phosphate Shuttle;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Fanconi-bickel syndrome;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Glycogenosis, Type IB;Cori Cycle;Alzheimers Disease;HIF1A and PPARG regulation of glycolysis;Pathways in clear cell renal cell carcinoma;Glycolysis and Gluconeogenesis;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;downregulated of mta-3 in er-negative breast tumors;Metabolism of carbohydrates;Glycolysis Gluconeogenesis;Metabolism;Glycolysis;gluconeogenesis;NADH repair;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Gluconeogenesis;Glucose metabolism;Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.991
Intolerance Scores
- loftool
- 0.617
- rvis_EVS
- -0.4
- rvis_percentile_EVS
- 26.53
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.709
- ghis
- 0.568
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gapdh
- 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); hematopoietic system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- microtubule cytoskeleton organization;gluconeogenesis;glycolytic process;negative regulation of endopeptidase activity;regulation of macroautophagy;negative regulation of translation;killing of cells of other organism;peptidyl-cysteine S-trans-nitrosylation;positive regulation of cytokine secretion;protein stabilization;defense response to fungus;neuron apoptotic process;killing by host of symbiont cells;positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction;canonical glycolysis;antimicrobial humoral immune response mediated by antimicrobial peptide;cellular response to interferon-gamma
- Cellular component
- nucleus;cytoplasm;lipid droplet;cytosol;plasma membrane;microtubule cytoskeleton;membrane;nuclear membrane;vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;extracellular exosome;GAIT complex;ribonucleoprotein complex
- Molecular function
- glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity;protein binding;microtubule binding;aspartic-type endopeptidase inhibitor activity;peptidyl-cysteine S-nitrosylase activity;identical protein binding;NADP binding;NAD binding;disordered domain specific binding