ENGASE

protein-coding

endo-beta-N-acetylglucosaminidase, the group of Glycoside hydrolases

Gene summary

This gene encodes a cytosolic enzyme which catalyzes the hydrolysis of peptides and proteins with mannose modifications to produce free oligosaccharides. [provided by RefSeq, Feb 2012]

MANE transcript

NM_001042573.3

Inheritance

—

ClinVar variants

U:142B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr17:79,074,824-79,088,599

External References & Databases

Ensembl (ENSG00000167280)

Transcript & Mutation Effects

hg38 • Region Span ~13.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ENGASE variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001042573.3. 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			3 clinvar	3 clinvar	1 clinvar	7
missense			133 clinvar	7 clinvar	2 clinvar	142
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	142	10	3	155

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001042573.3	RefSeq	NP_001036038.1	14	MANE Select
ENST00000579016.6	Ensembl	ENSP00000462333.1	14	MANE Select
NM_001396052.1	RefSeq	NP_001382981.1	13	Standard
NM_001396053.1	RefSeq	NP_001382982.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Other glycan degradation - Homo sapiens (human)
Post-translational protein modification
Metabolism of proteins
Asparagine N-linked glycosylation
N-glycan trimming in the ER and Calnexin/Calreticulin cycle

Biological Process

protein folding
protein deglycosylation

Molecular Function

mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000579016
Coding exons: 14
Length: 13661
Individuals with no LoFs: 124571
Homozygous LoFs: 0
Heterozygous LoFs: 359
Defined: 124930
p: 0.00144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0208	451	450	1.00	0.0000291	4748
Missense (PolyPhen)		139	145.6	0.95467		1603
Synonymous	-0.513	197	188	1.05	0.0000122	1544
Loss of Function	-0.0881	37	36.4	1.02	0.00000203	373

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0032	0.0030	notable
Latino/Admixed American	0.0015	0.0015	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0018	0.0018	notable
Finnish	0.0016	0.0016	notable
European (Non-Finnish)	0.0013	0.0013	notable
South Asian	0.0014	0.0013	notable
Other	0.0010	0.00099	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Endoglycosidase that releases N-glycans from glycoproteins by cleaving the beta-1,4-glycosidic bond in the N,N'-diacetylchitobiose core. Involved in the processing of free oligosaccharides in the cytosol. {ECO:0000269|PubMed:12114544}.;

Intolerance Scores

LoFtool: 0.894
RVIS EVS: -0.63
RVIS percentile EVS: 16.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.262

Gene Damage Prediction

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