TREH

protein-coding

trehalase, the group of Glycoside hydrolases

Gene summary

This gene encodes an enzyme that hydrolyses trehalose, a disaccharide formed from two glucose molecules found mainly in fungi, plants, and insects. A partial duplication of this gene is located adjacent to this locus on chromosome 11. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

MANE transcript

NM_007180.3

Inheritance

AD, AR

ClinVar variants

P:1U:91B:24

Top phenotype

Trehalase deficiency

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr11:118,657,316-118,679,690

External References & Databases

Ensembl (ENSG00000118094)

Transcript & Mutation Effects

hg38 • Region Span ~22.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

diarrhea-vomiting due to trehalase deficiencySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0012803

Submitter: Orphanet

Clinical Genomic Database (CGD)

Trehalase deficiencyAR

Manifestation: Biochemical

Intervention: General

Rationale: The clinical significance is unclear

Refs: 28406212

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TREH variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 91

TREH-related disorderTotal: 24

not providedTotal: 4

alpha, alpha-Trehalase deficiencyTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007180.3. 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				13 clinvar	1 clinvar	14
missense			88 clinvar	8 clinvar	2 clinvar	98
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar			2
Total	0	1	91	21	3	116

Highest pathogenic variant AF is 0.0007255028

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007180.3	RefSeq	NP_009111.2	15	MANE Select
ENST00000264029.9	Ensembl	ENSP00000264029.5	15	MANE Select
NM_001301065.2	RefSeq	NP_001287994.1	14	Standard
ENST00000397925.2	Ensembl	ENSP00000381020.2	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Starch and sucrose metabolism - Homo sapiens (human)
Trehalose Degradation
Digestion of dietary carbohydrate
trehalose degradation
Digestion

Biological Process

trehalose metabolic process
trehalose catabolic process
animal organ morphogenesis

Molecular Function

alpha,alpha-trehalase activity

Cellular Component

anchored component of membrane
anchored component of plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264029
Coding exons: 16
Length: 22374
Individuals with no LoFs: 124190
Homozygous LoFs: 4
Heterozygous LoFs: 497
Defined: 124691
p: 0.00201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.443	289	311	0.929	0.0000174	3677
Missense (PolyPhen)		100	122.02	0.81953		1525
Synonymous	0.346	123	128	0.961	0.00000721	1098
Loss of Function	1.46	27	36.5	0.740	0.00000183	399

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00067	0.00064	rare
Latino/Admixed American	0.00063	0.00061	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00024	0.00022	rare
Finnish	0.00053	0.00051	rare
European (Non-Finnish)	0.0015	0.0015	notable
South Asian	0.011	0.0091	notable
Other	0.0022	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Intestinal trehalase is probably involved in the hydrolysis of ingested trehalose. {ECO:0000269|PubMed:8773341, ECO:0000269|PubMed:9427547}.;

Recessive Scores

pRec: 0.425

Essentials

Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.804

Gene Damage Prediction

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