UGDH

UDP-glucose 6-dehydrogenase

Basic information

Region (hg38): 4:39498754-39528311

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.

• Epileptic encephalopathy (1 variants)
• Developmental and epileptic encephalopathy, 84 (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.

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				7		7
missense		3	16		1	20
nonsense	1		1			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1	1	3
non coding						0
Total	1	3	17	7	1

Highest pathogenic variant AF is 0.000112

Variants in UGDH

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

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

Position	Type	Phenotype	Significance	ClinVar
4-39500188-C-G			Likely benign (Feb 01, 2022)
4-39500189-G-C		Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
4-39500205-G-A		Inborn genetic diseases	Uncertain significance (Nov 01, 2023)
4-39500205-G-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2023)
4-39500207-G-A		Inborn genetic diseases	Uncertain significance (Sep 12, 2023)
4-39500232-C-T		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
4-39503903-T-C		Epileptic encephalopathy	Likely pathogenic (Oct 01, 2019)
4-39503921-C-T		Epileptic encephalopathy	Likely pathogenic (Oct 01, 2019)
4-39503925-G-A		Epileptic encephalopathy	Likely pathogenic (Oct 01, 2019)
4-39503957-T-C		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
4-39503978-TC-T		Inborn genetic diseases	Pathogenic (Jun 04, 2024)
4-39504452-C-A		Epileptic encephalopathy	Likely pathogenic (Oct 01, 2019)
4-39504503-G-A		Epileptic encephalopathy • Developmental and epileptic encephalopathy, 84	Likely pathogenic (Feb 23, 2023)
4-39505308-T-C		Epileptic encephalopathy • Developmental and epileptic encephalopathy, 84	Pathogenic/Likely pathogenic (Oct 07, 2020)
4-39505325-A-G			Likely benign (Aug 01, 2023)
4-39505340-A-C		Epileptic encephalopathy	Likely pathogenic (Oct 01, 2019)
4-39505377-G-GA			Likely benign (Jul 01, 2024)
4-39505705-C-T		Epileptic encephalopathy • Developmental and epileptic encephalopathy, 84	Pathogenic/Likely pathogenic (Jan 03, 2022)
4-39505706-G-A			Uncertain significance (Jun 15, 2022)
4-39505728-G-C		Developmental and epileptic encephalopathy, 84	Uncertain significance (Mar 14, 2024)
4-39505734-A-G			Likely benign (Jun 01, 2023)
4-39505739-T-C		Epileptic encephalopathy	Likely pathogenic (Oct 01, 2019)
4-39505748-C-T		Epileptic encephalopathy	Likely pathogenic (Oct 01, 2019)
4-39509760-C-G		Epileptic encephalopathy	Likely pathogenic (Oct 01, 2019)
4-39509779-C-T			Likely benign (Jul 01, 2024)

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