UGDH

UDP-glucose 6-dehydrogenase

Basic information

Region (hg38): 4:39498755-39528311

Links

ENSG00000109814

∙ NCBI:7358 ∙ OMIM:603370 ∙ HGNC:12525 ∙ Uniprot:O60701 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

developmental and epileptic encephalopathy, 84 (Strong), mode of inheritance: AR
developmental and epileptic encephalopathy, 84 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 84 (Jamuar syndrome)	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	32001716

ClinVar

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

Inborn_genetic_diseases (30 variants)
Epileptic_encephalopathy (23 variants)
not_provided (22 variants)
Developmental_and_epileptic_encephalopathy,_84 (21 variants)
UGDH-related_disorder (5 variants)
not_specified (1 variants)
West_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGDH gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003359.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar		8
missense		22 clinvar	45 clinvar	3 clinvar		70
nonsense	1 clinvar	2 clinvar	1 clinvar			4
start loss						0
frameshift	1 clinvar	1 clinvar				2
splice donor/acceptor (+/-2bp)						0
Total	2	25	46	11	0

Highest pathogenic variant AF is 0.00020398729

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGDH	protein_coding	protein_coding	ENST00000316423	11	29557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000683	0.996	125708	0	39	125747	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	164	271	0.606	0.0000141	3247
Missense in Polyphen		45	120.06	0.3748		1479
Synonymous	1.00	78	90.1	0.866	0.00000442	945
Loss of Function	2.53	9	21.8	0.414	9.84e-7	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000666	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000645	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000259	0.000246
Middle Eastern	0.0000645	0.0000544
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate.;
Pathway: Ascorbate and aldarate metabolism - Homo sapiens (human);Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Pentose and glucuronate interconversions - Homo sapiens (human);Galactosemia III;Galactosemia II (GALK);Glycogen synthetase deficiency;Glycogenosis, Type III. Cori disease, Debrancher glycogenosis;Mucopolysaccharidosis VI. Sly syndrome;Sucrase-isomaltase deficiency;Glycogenosis, Type IV. Amylopectinosis, Anderson disease;Glycogenosis, Type VI. Hers disease;Starch and Sucrose Metabolism;Nucleotide Sugars Metabolism;Glucuronidation;Formation of the active cofactor, UDP-glucuronate;Glucuronidation;Phase II - Conjugation of compounds;UDP-D-xylose and UDP-D-glucuronate biosynthesis;Biological oxidations;Metabolism (Consensus)

Recessive Scores

pRec: 0.110

Intolerance Scores

loftool: 0.461
rvis_EVS: -0.14
rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

pHI: 0.910
hipred: Y
hipred_score: 0.614
ghis: 0.538

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ugdh
Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; embryo phenotype; vision/eye phenotype;

Zebrafish Information Network

Gene name: ugdh
Affected structure: atrioventricular valve
Phenotype tag: abnormal
Phenotype quality: aplastic

Gene ontology

Biological process: gastrulation with mouth forming second;UDP-glucose metabolic process;glycosaminoglycan biosynthetic process;UDP-glucuronate biosynthetic process;electron transport chain
Cellular component: nucleus;nucleoplasm;cytosol;extracellular exosome
Molecular function: UDP-glucose 6-dehydrogenase activity;electron transfer activity;NAD binding