UGCG

UDP-glucose ceramide glucosyltransferase, the group of UDP-glucose ceramide glucosyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:111896814-111935369

Links

ENSG00000148154 ∙ NCBI:7357 ∙ OMIM:602874 ∙ HGNC:12524 ∙ Uniprot:Q16739 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ichthyosis (Limited), mode of inheritance: AR

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGCG 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in UGCG

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

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

Position	Type	Phenotype	Significance	ClinVar
9-111914619-A-G		not specified	Uncertain significance (Oct 13, 2023)
9-111914647-T-TA		Congenital nonbullous ichthyosiform erythroderma	Conflicting classifications of pathogenicity (Feb 09, 2023)
9-111914651-A-G		not specified	Uncertain significance (Mar 06, 2023)
9-111914663-G-A		not specified	Uncertain significance (Dec 26, 2023)
9-111914709-A-G		not specified	Uncertain significance (Jun 30, 2023)
9-111922895-A-G		not specified	Uncertain significance (Feb 15, 2023)
9-111926465-A-G		not specified	Uncertain significance (Mar 14, 2023)
9-111929545-G-T		not specified	Uncertain significance (Dec 20, 2023)
9-111931329-A-G		not specified	Uncertain significance (Aug 04, 2023)
9-111932245-T-A		not specified	Uncertain significance (Mar 31, 2023)
9-111932959-C-T		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGCG	protein_coding	protein_coding	ENST00000374279	9	38604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.941	0.0585	125736	0	6	125742	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	101	214	0.473	0.0000103	2590
Missense in Polyphen		11	56.61	0.19431		709
Synonymous	-0.636	79	72.1	1.10	0.00000361	731
Loss of Function	3.78	3	22.2	0.135	0.00000122	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the first glycosylation step in glycosphingolipid biosynthesis, the transfer of glucose to ceramide. May also serve as a "flippase". {ECO:0000269|PubMed:8643456}.
• Pathway: Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Fabry disease;Krabbe disease;Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism;IL2 signaling events mediated by PI3K (Consensus)

Recessive Scores

• pRec: 0.400

Intolerance Scores

• loftool: 0.215
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.728
• ghis: 0.526

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: Ugcg
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: glucosylceramide biosynthetic process;glycosphingolipid metabolic process;glycosphingolipid biosynthetic process;epidermis development
• Cellular component: Golgi membrane;membrane;integral component of membrane
• Molecular function: ceramide glucosyltransferase activity;dihydroceramide glucosyltransferase activity