TREX2

three prime repair exonuclease 2, the group of Exonucleases

Basic information

Region (hg38): X:153444473-153470587

Links

ENSG00000183479 ∙ NCBI:11219 ∙ OMIM:300370 ∙ HGNC:12270 ∙ Uniprot:Q9BQ50 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TREX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TREX2 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				7	1	8
missense			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	4	3	9
non coding			20	10	3	33
Total	0	0	38	20	4

Variants in TREX2

This is a list of pathogenic ClinVar variants found in the TREX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-153444753-G-A			Likely benign (Jul 01, 2022)
X-153444781-C-T		not specified	Uncertain significance (Mar 30, 2024)
X-153444782-G-A		not specified	Uncertain significance (Oct 12, 2022)
X-153444789-C-T			Likely benign (Jun 01, 2022)
X-153444807-C-T			Likely benign (Mar 01, 2023)
X-153444824-G-A		Intellectual disability	Uncertain significance (-)
X-153444875-C-T			Likely benign (Nov 01, 2022)
X-153444890-G-A		not specified	Conflicting classifications of pathogenicity (Nov 01, 2022)
X-153444890-G-T			Likely benign (Sep 01, 2022)
X-153444899-G-A		not specified	Uncertain significance (May 23, 2023)
X-153444984-C-T			Likely benign (Dec 01, 2022)
X-153444986-G-A		not specified	Uncertain significance (Sep 14, 2022)
X-153445005-A-G			Likely benign (Nov 01, 2022)
X-153445012-C-T		not specified	Likely benign (May 08, 2023)
X-153445034-G-A		not specified	Uncertain significance (May 09, 2023)
X-153445143-G-A			Likely benign (Jul 01, 2022)
X-153445166-G-A		not specified	Uncertain significance (Aug 14, 2023)
X-153445171-C-G		not specified	Uncertain significance (Feb 26, 2024)
X-153445172-G-A		Abnormality of neuronal migration	Likely benign (-)
X-153445174-G-A		not specified	Uncertain significance (Oct 12, 2021)
X-153445181-C-T		not specified	Uncertain significance (Jun 21, 2023)
X-153445196-C-T		not specified	Uncertain significance (Sep 14, 2022)
X-153445200-G-A			Benign (Dec 14, 2017)
X-153445205-C-T		not specified	Uncertain significance (Nov 07, 2022)
X-153445234-G-A		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TREX2	protein_coding	protein_coding	ENST00000330912	1	25868

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.454	0.457	124026	47	153	124226	0.000805

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.658	125	106	1.18	0.0000106	1451
Missense in Polyphen		39	33.389	1.1681		560
Synonymous	-1.24	59	48.1	1.23	0.00000454	527
Loss of Function	1.15	0	1.53	0.00	9.64e-8	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0146	0.0111
Ashkenazi Jewish	0.000463	0.000300
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000688	0.0000446
Middle Eastern	0.00	0.00
South Asian	0.0000595	0.0000329
Other	0.000713	0.000493

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exonuclease with a preference for double-stranded DNA with mismatched 3' termini. May play a role in DNA repair. {ECO:0000269|PubMed:11279105}.

Intolerance Scores

• loftool: 0.646
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0429
• hipred: N
• hipred_score: 0.170
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.777

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trex2
• Phenotype: neoplasm; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: DNA metabolic process;DNA repair;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus
• Molecular function: magnesium ion binding;nucleic acid binding;3'-5'-exodeoxyribonuclease activity;exodeoxyribonuclease III activity;protein homodimerization activity