EXD2

exonuclease 3'-5' domain containing 2

Basic information

Region (hg38): 14:69191498-69244020

Previous symbols: [ "C14orf114", "EXDL2" ]

Links

ENSG00000081177 ∙ NCBI:55218 ∙ OMIM:616940 ∙ HGNC:20217 ∙ Uniprot:Q9NVH0 ∙ 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 EXD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXD2 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				1		1
missense			42			42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	46	1	0

Variants in EXD2

This is a list of pathogenic ClinVar variants found in the EXD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-69209505-C-T		not specified	Uncertain significance (Sep 01, 2024)
14-69209558-C-T		not specified	Uncertain significance (Feb 27, 2023)
14-69209561-C-T		not specified	Uncertain significance (Nov 09, 2023)
14-69209562-G-C		not specified	Uncertain significance (Nov 12, 2024)
14-69209598-C-T		not specified	Uncertain significance (Jul 09, 2021)
14-69209609-G-T		not specified	Uncertain significance (Feb 12, 2024)
14-69209618-A-G		not specified	Uncertain significance (Mar 02, 2023)
14-69209669-A-G		not specified	Uncertain significance (Dec 15, 2023)
14-69209676-C-T		not specified	Uncertain significance (Jan 24, 2024)
14-69209687-C-T		not specified	Uncertain significance (Jul 14, 2021)
14-69209762-G-A		not specified	Uncertain significance (Nov 04, 2023)
14-69209775-T-C		not specified	Uncertain significance (Jan 23, 2024)
14-69209777-C-T		not specified	Uncertain significance (Oct 17, 2023)
14-69209778-C-G		not specified	Uncertain significance (Dec 06, 2024)
14-69228892-G-A		not specified	Uncertain significance (May 27, 2022)
14-69228910-G-A		not specified	Uncertain significance (May 27, 2022)
14-69228958-G-A		not specified	Uncertain significance (Nov 10, 2024)
14-69229026-G-C		not specified	Uncertain significance (Oct 12, 2024)
14-69229051-G-A		not specified	Uncertain significance (Feb 05, 2024)
14-69230476-A-T		not specified	Uncertain significance (Mar 06, 2023)
14-69230479-T-G		not specified	Uncertain significance (Jul 16, 2024)
14-69230509-C-T		not specified	Uncertain significance (Jul 19, 2022)
14-69230512-G-A		not specified	Uncertain significance (Feb 15, 2023)
14-69230552-T-C		not specified	Uncertain significance (Aug 05, 2024)
14-69230558-G-A		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXD2	protein_coding	protein_coding	ENST00000409018	8	50848

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.66e-12	0.297	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.933	295	344	0.858	0.0000194	4035
Missense in Polyphen		101	129.73	0.77855		1453
Synonymous	2.22	101	134	0.756	0.00000723	1239
Loss of Function	1.07	21	27.0	0.778	0.00000146	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000381	0.000381
Finnish	0.000233	0.000231
European (Non-Finnish)	0.000337	0.000281
Middle Eastern	0.000381	0.000381
South Asian	0.000163	0.000163
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exonuclease required for double-strand breaks resection and efficient homologous recombination. Plays a key role in controlling the initial steps of chromosomal break repair, it is recruited to chromatin in a damage-dependent manner and functionally interacts with the MRN complex to accelerate resection through its 3'-5' exonuclease activity, which efficiently processes double-stranded DNA substrates containing nicks. {ECO:0000269|PubMed:20603073, ECO:0000269|PubMed:26807646}.

Intolerance Scores

• loftool: 0.937
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.204
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.129

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exd2

Gene ontology

• Biological process: double-strand break repair via homologous recombination;DNA double-strand break processing;double-strand break repair;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;cytoplasm
• Molecular function: nucleic acid binding;protein binding;single-stranded DNA 3'-5' exodeoxyribonuclease activity;3'-5' exonuclease activity;exodeoxyribonuclease I activity