GLUD2
Basic information
Region (hg38): X:121047610-121050094
Previous symbols: [ "GLUDP1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
- not_provided (9 variants)
- Parkinson_disease,_late-onset (1 variants)
- Male_infertility_with_azoospermia_or_oligozoospermia_due_to_single_gene_mutation (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLUD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012084.4. 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 | 4 | |||||
| missense | 51 | 56 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 51 | 7 | 2 |
Highest pathogenic variant AF is 0.0002875767
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GLUD2 | protein_coding | protein_coding | ENST00000328078 | 1 | 2333 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0315 | 0.826 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.825 | 188 | 223 | 0.844 | 0.0000178 | 3665 |
| Missense in Polyphen | 40 | 66.994 | 0.59707 | 1149 | ||
| Synonymous | -0.399 | 93 | 88.2 | 1.05 | 0.00000688 | 1150 |
| Loss of Function | 1.15 | 3 | 6.05 | 0.496 | 3.90e-7 | 145 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Important for recycling the chief excitatory neurotransmitter, glutamate, during neurotransmission.;
- Pathway
- Alanine, aspartate and glutamate metabolism - Homo sapiens (human);D-Glutamine and D-glutamate metabolism - Homo sapiens (human);Proximal tubule bicarbonate reclamation - Homo sapiens (human);Necroptosis - Homo sapiens (human);Nitrogen metabolism - Homo sapiens (human);Arginine biosynthesis - Homo sapiens (human);Glutamate Glutamine metabolism;Metabolism of amino acids and derivatives;Metabolism;ornithine <i>de novo </i> biosynthesis;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Arginine Proline metabolism;glutamate biosynthesis/degradation;GABA shunt;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Amino acid synthesis and interconversion (transamination);Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.620
Intolerance Scores
- loftool
- 0.0904
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.51
Haploinsufficiency Scores
- pHI
- 0.121
- hipred
- N
- hipred_score
- 0.187
- ghis
- 0.559
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- glutamate metabolic process;glutamate biosynthetic process;glutamate catabolic process;oxidation-reduction process
- Cellular component
- cytoplasm;mitochondrion
- Molecular function
- glutamate dehydrogenase (NAD+) activity;glutamate dehydrogenase [NAD(P)+] activity;GTP binding;ADP binding;leucine binding