UGCG

protein-coding

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

Gene summary

This gene encodes an enzyme that catalyzes the first glycosylation step in the biosynthesis of glycosphingolipids, which are membrane components containing lipid and sugar moieties. The product of this reaction is glucosylceramide, which is the core structure of many glycosphingolipids. [provided by RefSeq, Dec 2014]

MANE transcript

NM_003358.3

Inheritance

ClinVar variants

P:1U:30

Top phenotype

Congenital nonbullous ichthyosiform erythroderma

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr9:111,896,814-111,935,369

External References & Databases

Ensembl (ENSG00000148154)

Transcript & Mutation Effects

hg38 • Region Span ~38.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

ichthyosisLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019269

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UGCG variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 1

Congenital nonbullous ichthyosiform erythrodermaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003358.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			28 clinvar			28
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	30	0	0	31

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003358.3	RefSeq	NP_003349.1	9	MANE Select
ENST00000374279.4	Ensembl	ENSP00000363397.3	9	MANE Select
ENST00000856545.1	Ensembl	ENSP00000526604.1	8	Standard
ENST00000856545.2	Ensembl	ENSP00000526604.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Sphingolipid metabolism - Homo sapiens (human)
Sphingolipid Metabolism
Gaucher Disease
Globoid Cell Leukodystrophy
Metachromatic Leukodystrophy (MLD)

Biological Process

glucosylceramide biosynthetic process
glycosphingolipid metabolic process
glycosphingolipid biosynthetic process
epidermis development

Molecular Function

ceramide glucosyltransferase activity
dihydroceramide glucosyltransferase activity

Cellular Component

Golgi membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374279
Coding exons: 9
Length: 38604
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125742
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.74	101	214	0.473	0.0000103	2590
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.400

Intolerance Scores

LoFtool: 0.215
RVIS EVS: -0.05
RVIS percentile EVS: 49.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.976

Gene Damage Prediction

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