CTBS

protein-coding

chitobiase, the group of Chitinases

Gene summary

Chitobiase is a lysosomal glycosidase involved in degradation of asparagine-linked oligosaccharides on glycoproteins (Aronson and Kuranda, 1989 [PubMed 2531691]).[supplied by OMIM, Nov 2010]

Previous symbols:

MANE transcript

NM_004388.3

Inheritance

—

ClinVar variants

U:59B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr1:84,549,611-84,574,480

External References & Databases

Ensembl (ENSG00000117151)

Transcript & Mutation Effects

hg38 • Region Span ~24.9 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 CTBS variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004388.3. 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					2 clinvar	2
missense			58 clinvar	6 clinvar	1 clinvar	65
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	59	6	3	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004388.3	RefSeq	NP_004379.1	7	MANE Select
ENST00000370630.6	Ensembl	ENSP00000359664.4	7	MANE Select
ENST00000370625.1	Ensembl	ENSP00000359659.1	1	Standard
ENST00000465118.6	Ensembl	ENSP00000452177.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chitin catabolic process
oligosaccharide catabolic process

Molecular Function

chitinase activity
chitin binding

Cellular Component

extracellular space
lysosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370630
Coding exons: 7
Length: 24875
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125742
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.659	180	207	0.871	0.0000101	2473
Missense (PolyPhen)		40	51.364	0.77876		653
Synonymous	2.21	49	73.0	0.671	0.00000348	714
Loss of Function	1.00	13	17.5	0.741	7.40e-7	228

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the degradation of asparagine-linked glycoproteins. Hydrolyze of N-acetyl-beta-D-glucosamine (1-4)N- acetylglucosamine chitobiose core from the reducing end of the bond, it requires prior cleavage by glycosylasparaginase.;

Recessive Scores

pRec: 0.342

Intolerance Scores

LoFtool: 0.905
RVIS EVS: -0.05
RVIS percentile EVS: 50.22

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.982

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High