DHDH

dihydrodiol dehydrogenase

Basic information

Region (hg38): 19:48933698-48944969

Links

ENSG00000104808 ∙ NCBI:27294 ∙ OMIM:606377 ∙ HGNC:17887 ∙ Uniprot:Q9UQ10 ∙ 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 DHDH gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DHDH 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in DHDH

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

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

Position	Type	Phenotype	Significance	ClinVar
19-48933752-G-A		not specified	Uncertain significance (Aug 21, 2023)
19-48935022-A-C		not specified	Uncertain significance (Dec 19, 2022)
19-48935075-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-48936062-A-G		not specified	Uncertain significance (Nov 18, 2022)
19-48936095-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-48936100-A-C		not specified	Uncertain significance (Nov 28, 2023)
19-48936112-T-A		not specified	Uncertain significance (Aug 02, 2021)
19-48936149-G-A		not specified	Uncertain significance (Mar 21, 2023)
19-48939452-A-G		not specified	Uncertain significance (Dec 13, 2022)
19-48939467-T-G		not specified	Uncertain significance (Aug 14, 2023)
19-48939482-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-48939489-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-48939551-A-T		not specified	Uncertain significance (Oct 27, 2022)
19-48939564-T-A		not specified	Uncertain significance (Jan 20, 2023)
19-48939581-C-T		not specified	Likely benign (Oct 06, 2021)
19-48939593-G-C		not specified	Uncertain significance (Aug 16, 2021)
19-48939611-A-G		not specified	Uncertain significance (Dec 17, 2023)
19-48939631-G-C		not specified	Uncertain significance (Aug 12, 2022)
19-48939672-T-G		not specified	Uncertain significance (Nov 03, 2022)
19-48939674-T-A		not specified	Uncertain significance (Jan 05, 2022)
19-48939693-A-T		Malignant tumor of prostate	Uncertain significance (-)
19-48942514-G-A		not specified	Uncertain significance (Nov 23, 2021)
19-48942538-G-A		not specified	Uncertain significance (Aug 22, 2022)
19-48944370-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-48944376-G-A		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DHDH	protein_coding	protein_coding	ENST00000221403	7	11288

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.13e-10	0.0869	68402	8106	49240	125748	0.262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0990	208	212	0.981	0.0000134	2134
Missense in Polyphen		65	67.443	0.96377		745
Synonymous	-0.144	94	92.2	1.02	0.00000649	686
Loss of Function	0.0397	14	14.2	0.989	7.66e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.501	0.488
Ashkenazi Jewish	0.166	0.146
East Asian	0.638	0.585
Finnish	0.577	0.369
European (Non-Finnish)	0.290	0.212
Middle Eastern	0.638	0.585
South Asian	0.413	0.351
Other	0.313	0.236

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Pentose and glucuronate interconversions - Homo sapiens (human);Benzene metabolism (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.878
• rvis_EVS: 1.76
• rvis_percentile_EVS: 96.71

Haploinsufficiency Scores

• pHI: 0.270
• hipred: N
• hipred_score: 0.197
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.800

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Dhdh

Gene ontology

• Biological process: carbohydrate metabolic process;electron transport chain;D-xylose catabolic process
• Molecular function: NAD(P)+ transhydrogenase activity;electron transfer activity;trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity;D-xylose 1-dehydrogenase (NADP+) activity