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GeneBe

BDH1

3-hydroxybutyrate dehydrogenase 1, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 3:197509782-197573323

Previous symbols: [ "BDH" ]

Links

ENSG00000161267NCBI:622OMIM:603063HGNC:1027Uniprot:Q02338AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BDH1 gene.

  • Inborn genetic diseases (16 variants)
  • not provided (5 variants)
  • BDH1-related condition (1 variants)

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
clinvar
2
missense
15
clinvar
2
clinvar
3
clinvar
20
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 15 2 5

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)2227005
3-197511909-T-C not specified Uncertain significance (Jan 23, 2023)3133583
3-197511910-C-T not specified Uncertain significance (Aug 02, 2023)2615668
3-197511986-C-T BDH1-related condition Likely benign (Jul 14, 2022)3052892
3-197512014-C-T not specified Uncertain significance (Jan 19, 2022)2210193
3-197512079-T-A not specified Uncertain significance (Apr 08, 2022)2383361
3-197512122-G-A not specified Uncertain significance (Jul 07, 2022)2299959
3-197512183-G-A Benign (Aug 16, 2018)791966
3-197512185-A-G not specified Uncertain significance (Dec 01, 2022)2330258
3-197512224-C-G not specified Uncertain significance (Dec 23, 2022)2393313
3-197512284-C-T BDH1-related condition Benign (Dec 31, 2019)715597
3-197512286-C-G not specified Uncertain significance (Oct 12, 2022)3133595
3-197512293-T-G not specified Uncertain significance (Sep 14, 2023)2624392
3-197512301-C-T not specified Uncertain significance (Aug 02, 2022)2375586
3-197512314-G-A not specified Uncertain significance (Feb 26, 2024)3133594
3-197512319-G-A not specified Uncertain significance (Oct 27, 2023)3133593
3-197512340-A-G not specified Uncertain significance (Jun 07, 2023)2558826
3-197512353-T-C BDH1-related condition Uncertain significance (Sep 08, 2022)2631871
3-197512356-C-T not specified Uncertain significance (Oct 25, 2023)3133592
3-197512361-C-T not specified Uncertain significance (Jun 01, 2023)2515248
3-197514299-G-A not specified Uncertain significance (Aug 20, 2023)2596663
3-197514305-C-T not specified Uncertain significance (Dec 01, 2023)3133590
3-197514369-C-T not specified Uncertain significance (Aug 11, 2022)2306445
3-197514375-C-T not specified Uncertain significance (Dec 14, 2021)2267135
3-197514380-G-A not specified Uncertain significance (Sep 25, 2023)3133589

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BDH1protein_codingprotein_codingENST00000392379 663541
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.57e-80.28612564801001257480.000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4132122300.9230.00001492228
Missense in Polyphen7188.3580.80355887
Synonymous-0.2129794.41.030.00000651692
Loss of Function0.4881214.00.8597.56e-7168

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009700.000970
Ashkenazi Jewish0.0001030.0000992
East Asian0.002990.00299
Finnish0.00004620.0000462
European (Non-Finnish)0.0001690.000167
Middle Eastern0.002990.00299
South Asian0.0001310.000131
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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