TREH

trehalase, the group of Glycoside hydrolases

Basic information

Region (hg38): 11:118657315-118679690

Links

ENSG00000118094 ∙ NCBI:11181 ∙ OMIM:275360 ∙ HGNC:12266 ∙ Uniprot:O43280 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• diarrhea-vomiting due to trehalase deficiency (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Trehalase deficiency	AR	General	The clinical significance is unclear	Biochemical	28406212

ClinVar

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

• Inborn genetic diseases (30 variants)
• not provided (3 variants)
• alpha, alpha-Trehalase deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TREH 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			28	4		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	28	4	1

Variants in TREH

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

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

Position	Type	Phenotype	Significance	ClinVar
11-118658307-G-G			Benign (Sep 04, 2018)
11-118658345-G-A		TREH-related disorder • not specified	Conflicting classifications of pathogenicity (Sep 26, 2022)
11-118658348-G-T		not specified	Uncertain significance (Dec 09, 2023)
11-118658383-C-T		not specified	Uncertain significance (May 24, 2023)
11-118658416-A-T		not specified	Uncertain significance (Nov 07, 2023)
11-118658418-G-A		TREH-related disorder	Benign (Oct 21, 2019)
11-118658438-C-T		not specified	Uncertain significance (Apr 13, 2023)
11-118658685-C-T		not specified	Uncertain significance (Jun 22, 2021)
11-118658689-A-G		TREH-related disorder	Likely benign (Mar 14, 2019)
11-118658691-A-G		not specified	Uncertain significance (Sep 22, 2022)
11-118658705-C-T		not specified	Uncertain significance (Aug 30, 2021)
11-118658724-T-C		not specified	Uncertain significance (Aug 10, 2021)
11-118658915-A-G		TREH-related disorder	Likely benign (Aug 28, 2019)
11-118658925-T-A		TREH-related disorder	Uncertain significance (Feb 29, 2024)
11-118658926-C-A		TREH-related disorder • not specified	Uncertain significance (Feb 29, 2024)
11-118658955-T-C		not specified	Uncertain significance (Jan 22, 2024)
11-118658993-C-T		TREH-related disorder • not specified	Conflicting classifications of pathogenicity (Sep 14, 2021)
11-118659427-C-T		not specified	Uncertain significance (Nov 29, 2021)
11-118659447-G-A		not specified	Uncertain significance (Jul 12, 2022)
11-118659457-A-G			Likely benign (Oct 11, 2016)
11-118659761-G-C		not specified	Uncertain significance (Aug 12, 2022)
11-118659776-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-118659835-C-T		not specified	Likely benign (Dec 19, 2023)
11-118659902-T-C		TREH-related disorder	Benign (Oct 21, 2019)
11-118659912-G-A		TREH-related disorder	Likely benign (Aug 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TREH	protein_coding	protein_coding	ENST00000264029	16	22374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.96e-15	0.410	124190	4	497	124691	0.00201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.443	289	311	0.929	0.0000174	3677
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00130	0.00127
Ashkenazi Jewish	0.00	0.00
East Asian	0.000244	0.000222
Finnish	0.000530	0.000511
European (Non-Finnish)	0.00150	0.00148
Middle Eastern	0.000244	0.000222
South Asian	0.0112	0.00906
Other	0.00218	0.00198

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Intestinal trehalase is probably involved in the hydrolysis of ingested trehalose. {ECO:0000269|PubMed:8773341, ECO:0000269|PubMed:9427547}.
• Pathway: Starch and sucrose metabolism - Homo sapiens (human);Trehalose Degradation;Digestion of dietary carbohydrate;trehalose degradation;Digestion;Digestion and absorption (Consensus)

Recessive Scores

• pRec: 0.425

Haploinsufficiency Scores

• pHI: 0.347
• hipred: N
• hipred_score: 0.197
• ghis: 0.403

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.804

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Treh
• Phenotype: homeostasis/metabolism phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: trehalose metabolic process;trehalose catabolic process;animal organ morphogenesis
• Cellular component: anchored component of membrane;anchored component of plasma membrane;extracellular exosome
• Molecular function: alpha,alpha-trehalase activity