BDH1
Basic information
Region (hg38): 3:197509782-197573323
Previous symbols: [ "BDH" ]
Links
Phenotypes
GenCC
Source:
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 BDH1 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 | 2 | |||||
missense | 26 | 34 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 1 | 1 | ||||
non coding ? | 2 | |||||
Total | 0 | 0 | 26 | 6 | 6 |
Variants in BDH1
This is a list of pathogenic ClinVar variants found in the BDH1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-197511899-C-T | not specified | Likely benign (Jul 13, 2022) | ||
3-197511909-T-C | not specified | Uncertain significance (Jan 23, 2023) | ||
3-197511910-C-T | not specified | Uncertain significance (Aug 02, 2023) | ||
3-197511986-C-T | BDH1-related disorder | Likely benign (Jul 14, 2022) | ||
3-197512014-C-T | not specified | Uncertain significance (May 24, 2024) | ||
3-197512079-T-A | not specified | Uncertain significance (Apr 08, 2022) | ||
3-197512122-G-A | not specified | Uncertain significance (Jul 07, 2022) | ||
3-197512183-G-A | Benign (Aug 16, 2018) | |||
3-197512185-A-G | not specified | Uncertain significance (Dec 01, 2022) | ||
3-197512200-C-T | not specified | Uncertain significance (Mar 28, 2024) | ||
3-197512224-C-G | not specified | Uncertain significance (Dec 23, 2022) | ||
3-197512284-C-T | BDH1-related disorder | Benign (Dec 31, 2019) | ||
3-197512286-C-G | not specified | Uncertain significance (Oct 12, 2022) | ||
3-197512293-T-G | not specified | Uncertain significance (Sep 14, 2023) | ||
3-197512301-C-T | not specified | Uncertain significance (Aug 02, 2022) | ||
3-197512314-G-A | not specified | Uncertain significance (Feb 26, 2024) | ||
3-197512319-G-A | not specified | Uncertain significance (Oct 27, 2023) | ||
3-197512326-C-T | not specified | Uncertain significance (May 29, 2024) | ||
3-197512340-A-G | not specified | Uncertain significance (Jun 07, 2023) | ||
3-197512343-C-G | not specified | Uncertain significance (May 30, 2024) | ||
3-197512353-T-C | BDH1-related disorder | Uncertain significance (Sep 08, 2022) | ||
3-197512356-C-T | not specified | Uncertain significance (Oct 25, 2023) | ||
3-197512361-C-T | not specified | Uncertain significance (Jun 01, 2023) | ||
3-197514299-G-A | not specified | Uncertain significance (Aug 20, 2023) | ||
3-197514305-C-T | not specified | Uncertain significance (Dec 01, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
BDH1 | protein_coding | protein_coding | ENST00000392379 | 6 | 63541 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
7.57e-8 | 0.286 | 125648 | 0 | 100 | 125748 | 0.000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.413 | 212 | 230 | 0.923 | 0.0000149 | 2228 |
Missense in Polyphen | 71 | 88.358 | 0.80355 | 887 | ||
Synonymous | -0.212 | 97 | 94.4 | 1.03 | 0.00000651 | 692 |
Loss of Function | 0.488 | 12 | 14.0 | 0.859 | 7.56e-7 | 168 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000970 | 0.000970 |
Ashkenazi Jewish | 0.000103 | 0.0000992 |
East Asian | 0.00299 | 0.00299 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000169 | 0.000167 |
Middle Eastern | 0.00299 | 0.00299 |
South Asian | 0.000131 | 0.000131 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Butanoate metabolism - Homo sapiens (human);Synthesis and degradation of ketone bodies - Homo sapiens (human);Succinyl CoA: 3-ketoacid CoA transferase deficiency;Ketone Body Metabolism;Synthesis and Degradation of Ketone Bodies;ketogenesis;ketolysis;Butanoate metabolism;Metabolism of lipids;TCR;Metabolism;Synthesis of Ketone Bodies;Utilization of Ketone Bodies;Ketone body metabolism;Butanoate metabolism;FOXA2 and FOXA3 transcription factor networks
(Consensus)
Recessive Scores
- pRec
- 0.269
Intolerance Scores
- loftool
- 0.134
- rvis_EVS
- 0.42
- rvis_percentile_EVS
- 77.16
Haploinsufficiency Scores
- pHI
- 0.163
- hipred
- N
- hipred_score
- 0.289
- ghis
- 0.448
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.955
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bdh1
- Phenotype
Gene ontology
- Biological process
- ketone body biosynthetic process;ketone body catabolic process;oxidation-reduction process
- Cellular component
- nucleoplasm;mitochondrion;mitochondrial matrix;matrix side of mitochondrial inner membrane
- Molecular function
- 3-hydroxybutyrate dehydrogenase activity