D2HGDH
Basic information
Region (hg38): 2:241734602-241768816
Links
Phenotypes
GenCC
Source:
- D-2-hydroxyglutaric aciduria 1 (Limited), mode of inheritance: AR
- D-2-hydroxyglutaric aciduria (Supportive), mode of inheritance: AD
- D-2-hydroxyglutaric aciduria 1 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
D-2-hydroxyglutaric aciduria 1 | 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 | Biochemical; Cardiovascular; Neurologic | 15609246; 19169842; 20020533 |
ClinVar
This is a list of variants' phenotypes submitted to
- D-2-hydroxyglutaric aciduria 1 (9 variants)
- not provided (2 variants)
- D-2-hydroxyglutaric aciduria (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the D2HGDH 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 | 78 | 84 | ||||
missense | 107 | 118 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 9 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 6 | |||||
splice region | 2 | 6 | 1 | 9 | ||
non coding | 43 | 24 | 41 | 108 | ||
Total | 12 | 4 | 157 | 111 | 45 |
Highest pathogenic variant AF is 0.0000985
Variants in D2HGDH
This is a list of pathogenic ClinVar variants found in the D2HGDH region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-241734647-C-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 12, 2018) | ||
2-241734653-C-A | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 13, 2018) | ||
2-241734656-C-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 12, 2018) | ||
2-241734683-G-A | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 13, 2018) | ||
2-241734686-G-A | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 12, 2018) | ||
2-241734689-A-G | D-2-hydroxyglutaric aciduria 1 | Benign (Jan 12, 2018) | ||
2-241734690-T-G | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 12, 2018) | ||
2-241734710-C-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 13, 2018) | ||
2-241734898-A-C | Benign (May 11, 2021) | |||
2-241734936-C-G | Benign (May 11, 2021) | |||
2-241734937-C-G | Benign (May 11, 2021) | |||
2-241735129-C-G | not specified • D-2-hydroxyglutaric aciduria 1 | Conflicting classifications of pathogenicity (Jan 13, 2018) | ||
2-241735131-A-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jul 27, 2017) | ||
2-241735134-C-G | D-2-hydroxyglutaric aciduria 1 | Benign (May 11, 2021) | ||
2-241735142-C-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 13, 2018) | ||
2-241735180-C-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 12, 2018) | ||
2-241735188-C-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jan 12, 2018) | ||
2-241735230-G-A | D-2-hydroxyglutaric aciduria 1 | Likely benign (Aug 15, 2022) | ||
2-241735230-G-GC | D-2-hydroxyglutaric aciduria 1 | Likely pathogenic (Mar 29, 2024) | ||
2-241735235-G-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Jun 19, 2022) | ||
2-241735253-C-T | D-2-hydroxyglutaric aciduria 1 | Uncertain significance (Sep 13, 2022) | ||
2-241735261-C-T | D-2-hydroxyglutaric aciduria 1 | Likely benign (Aug 28, 2023) | ||
2-241735263-G-A | D-2-hydroxyglutaric aciduria 1 | Likely benign (Jul 28, 2023) | ||
2-241735267-C-A | D-2-hydroxyglutaric aciduria 1 | Likely benign (Nov 02, 2023) | ||
2-241735267-C-G | not specified • D-2-hydroxyglutaric aciduria 1 | Benign/Likely benign (Jan 30, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
D2HGDH | protein_coding | protein_coding | ENST00000321264 | 9 | 34238 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0543 | 0.945 | 125715 | 0 | 33 | 125748 | 0.000131 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.718 | 300 | 337 | 0.890 | 0.0000214 | 3288 |
Missense in Polyphen | 80 | 111.33 | 0.71858 | 1115 | ||
Synonymous | -0.543 | 172 | 163 | 1.05 | 0.0000119 | 1138 |
Loss of Function | 2.95 | 6 | 20.4 | 0.295 | 9.37e-7 | 223 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000606 | 0.000605 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000231 | 0.000231 |
European (Non-Finnish) | 0.0000357 | 0.0000352 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000233 | 0.000229 |
Other | 0.000663 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the oxidation of D-2-hydroxyglutarate to alpha-ketoglutarate. {ECO:0000269|PubMed:15070399}.;
- Disease
- DISEASE: D-2-hydroxyglutaric aciduria 1 (D2HGA1) [MIM:600721]: A rare recessive neurometabolic disorder causing developmental delay, epilepsy, hypotonia, and dysmorphic features. Both a mild and a severe phenotype exist. The severe phenotype is homogeneous and is characterized by early infantile-onset epileptic encephalopathy and cardiomyopathy. The mild phenotype has a more variable clinical presentation. Diagnosis is based on the presence of an excess of D-2-hydroxyglutaric acid in the urine. {ECO:0000269|PubMed:15609246, ECO:0000269|PubMed:16037974, ECO:0000269|PubMed:16081310}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- The oncogenic action of D-2-hydroxyglutarate in Hydroxygluaricaciduria ;Interconversion of 2-oxoglutarate and 2-hydroxyglutarate;Pyruvate metabolism and Citric Acid (TCA) cycle;The citric acid (TCA) cycle and respiratory electron transport;Metabolism
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.0903
- rvis_EVS
- -0.06
- rvis_percentile_EVS
- 48.84
Haploinsufficiency Scores
- pHI
- 0.261
- hipred
- N
- hipred_score
- 0.425
- ghis
- 0.482
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.171
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- D2hgdh
- Phenotype
Gene ontology
- Biological process
- 2-oxoglutarate metabolic process;response to manganese ion;response to zinc ion;lactate oxidation;respiratory electron transport chain;response to cobalt ion;response to magnesium ion;cellular protein metabolic process;response to calcium ion
- Cellular component
- mitochondrion;mitochondrial matrix;extrinsic component of cytoplasmic side of plasma membrane
- Molecular function
- D-lactate dehydrogenase (cytochrome) activity;(R)-2-hydroxyglutarate dehydrogenase activity;FAD binding