BDH1

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

Basic information

Region (hg38): 3:197509783-197573323

Previous symbols: [ "BDH" ]

Links

ENSG00000161267 ∙ NCBI:622 ∙ OMIM:603063 ∙ HGNC:1027 ∙ Uniprot:Q02338 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	2
missense			26	4	4	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				2		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: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bdh1

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