BDH2

3-hydroxybutyrate dehydrogenase 2, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 4:103077592-103099870

Previous symbols: [ "DHRS6" ]

Links

ENSG00000164039 ∙ NCBI:56898 ∙ ∙ HGNC:32389 ∙ Uniprot:Q9BUT1 ∙ 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 BDH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BDH2 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					1	1
missense			15		1	16
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	0	2

Variants in BDH2

This is a list of pathogenic ClinVar variants found in the BDH2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-103082094-A-G		not specified	Uncertain significance (Jun 11, 2024)
4-103082101-C-T		not specified	Uncertain significance (Oct 13, 2023)
4-103082132-G-T		not specified	Uncertain significance (Jan 04, 2024)
4-103082165-A-T		not specified	Uncertain significance (Nov 07, 2022)
4-103082170-G-A		not specified	Uncertain significance (May 21, 2024)
4-103082916-C-T			Benign (Apr 16, 2018)
4-103085365-G-C		not specified	Uncertain significance (Aug 21, 2024)
4-103085421-C-T		not specified	Uncertain significance (Oct 14, 2021)
4-103085432-G-A		not specified	Uncertain significance (Nov 27, 2024)
4-103091220-T-A		not specified	Uncertain significance (Jun 11, 2021)
4-103091245-C-T		not specified	Uncertain significance (Aug 04, 2023)
4-103091271-C-T		not specified	Uncertain significance (Feb 07, 2023)
4-103091281-C-G		not specified	Uncertain significance (May 29, 2024)
4-103092656-T-G		not specified	Uncertain significance (Jan 30, 2024)
4-103092675-T-A		not specified	Uncertain significance (Feb 17, 2022)
4-103095205-G-A		not specified	Uncertain significance (Jun 11, 2021)
4-103095212-T-C		not specified	Uncertain significance (Nov 13, 2023)
4-103095241-A-T		not specified	Uncertain significance (Aug 01, 2024)
4-103095267-T-G			Benign (Apr 16, 2018)
4-103095274-G-A		not specified	Uncertain significance (Dec 21, 2023)
4-103096188-C-G		not specified	Uncertain significance (Jan 17, 2023)
4-103096215-C-T		not specified	Uncertain significance (Dec 09, 2024)
4-103096247-C-T		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BDH2	protein_coding	protein_coding	ENST00000296424	9	20449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.53e-8	0.304	125601	1	146	125748	0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.496	121	137	0.881	0.00000724	1604
Missense in Polyphen		59	57.587	1.0245		677
Synonymous	1.60	33	46.9	0.703	0.00000260	459
Loss of Function	0.525	12	14.1	0.849	6.65e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000458	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00307	0.00301
European (Non-Finnish)	0.000292	0.000281
Middle Eastern	0.000544	0.000544
South Asian	0.000823	0.000817
Other	0.000987	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dehydrogenase that mediates the formation of 2,5- dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin and associates with LCN2, thereby playing a key role in iron homeostasis and transport. Also acts as a 3-hydroxybutyrate dehydrogenase (By similarity). {ECO:0000250, ECO:0000269|PubMed:16380372}.
• Pathway: Butanoate metabolism - Homo sapiens (human);Synthesis and degradation of ketone bodies - Homo sapiens (human);ketogenesis;ketolysis;Metabolism of lipids;Metabolism;Synthesis of Ketone Bodies;Ketone body metabolism;Butanoate metabolism (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.873
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.352
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bdh2
• Phenotype: hematopoietic system phenotype

Zebrafish Information Network

• Gene name: bdh2
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: fatty acid beta-oxidation;siderophore biosynthetic process;epithelial cell differentiation;heme metabolic process;ketone body biosynthetic process;iron ion homeostasis
• Cellular component: cytoplasm;mitochondrion;cytosol;extracellular exosome
• Molecular function: 3-hydroxybutyrate dehydrogenase activity;oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor;NAD binding