HIBADH

3-hydroxyisobutyrate dehydrogenase

Basic information

Region (hg38): 7:27525442-27662883

Links

ENSG00000106049 ∙ NCBI:11112 ∙ OMIM:608475 ∙ HGNC:4907 ∙ Uniprot:P31937 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 3-hydroxyisobutyric aciduria (Limited), mode of inheritance: AR

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIBADH 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						0
missense			17	1		18
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in HIBADH

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

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

Position	Type	Phenotype	Significance	ClinVar
7-27531245-C-T		not specified	Uncertain significance (Feb 28, 2023)
7-27531296-G-A		not specified	Uncertain significance (Dec 01, 2022)
7-27531323-C-A		HIBADH-related disorder	Likely benign (Feb 22, 2023)
7-27531334-G-T		not specified	Uncertain significance (Jan 18, 2022)
7-27538378-T-C		not specified	Uncertain significance (May 05, 2023)
7-27538416-G-T		not specified	Uncertain significance (Jun 22, 2021)
7-27543001-T-C		not specified	Uncertain significance (Jun 27, 2022)
7-27543002-T-TG			Uncertain significance (Nov 01, 2018)
7-27543014-A-G			Uncertain significance (Aug 01, 2023)
7-27543070-G-A		not specified	Uncertain significance (May 17, 2023)
7-27543085-C-A		not specified	Uncertain significance (May 14, 2024)
7-27629421-T-C		not specified	Uncertain significance (Dec 06, 2021)
7-27649480-C-T		not specified	Uncertain significance (Apr 11, 2023)
7-27649496-C-T		not specified	Uncertain significance (Oct 16, 2023)
7-27649573-C-T		not specified	Uncertain significance (Mar 31, 2024)
7-27649592-T-C		not specified	Uncertain significance (Apr 01, 2024)
7-27662700-G-A		not specified	Uncertain significance (Sep 13, 2023)
7-27662716-C-A			Uncertain significance (Aug 01, 2023)
7-27662718-G-A		not specified	Uncertain significance (Aug 17, 2021)
7-27662721-G-A		not specified	Uncertain significance (Feb 06, 2024)
7-27662758-C-T		not specified	Uncertain significance (Feb 26, 2024)
7-27662767-G-A		not specified	Uncertain significance (Mar 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIBADH	protein_coding	protein_coding	ENST00000265395	8	137554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00563	0.974	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.131	167	172	0.972	0.00000833	2156
Missense in Polyphen		46	65.601	0.70121		779
Synonymous	-0.499	67	62.0	1.08	0.00000321	681
Loss of Function	2.02	6	14.2	0.422	6.94e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000535	0.0000527
Middle Eastern	0.0000545	0.0000544
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Valine, leucine and isoleucine degradation - Homo sapiens (human);3-Methylglutaconic Aciduria Type I;Valine, Leucine and Isoleucine Degradation;2-Methyl-3-Hydroxybutryl CoA Dehydrogenase Deficiency;Isovaleric Aciduria;3-Methylcrotonyl Coa Carboxylase Deficiency Type I;Propionic Acidemia;Maple Syrup Urine Disease;3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency;Isobutyryl-coa dehydrogenase deficiency;3-hydroxyisobutyric aciduria;3-hydroxyisobutyric acid dehydrogenase deficiency;Isovaleric acidemia;Methylmalonate Semialdehyde Dehydrogenase Deficiency;Methylmalonic Aciduria;3-Methylglutaconic Aciduria Type IV;3-Methylglutaconic Aciduria Type III;Beta-Ketothiolase Deficiency;Amino Acid metabolism;Branched-chain amino acid catabolism;Metabolism of amino acids and derivatives;Metabolism;valine degradation;Valine, leucine and isoleucine degradation;Valine Leucine Isoleucine degradation (Consensus)

Recessive Scores

• pRec: 0.290

Intolerance Scores

• loftool: 0.572
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.367
• hipred: Y
• hipred_score: 0.565
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hibadh
• Phenotype: hematopoietic system phenotype; immune system phenotype; skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: valine catabolic process;branched-chain amino acid catabolic process;oxidation-reduction process
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: 3-hydroxyisobutyrate dehydrogenase activity;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;NADP binding;NAD binding