EXD3

exonuclease 3'-5' domain containing 3

Basic information

Region (hg38): 9:137306895-137423211

Links

ENSG00000187609 ∙ NCBI:54932 ∙ ∙ HGNC:26023 ∙ Uniprot:Q8N9H8 ∙ 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 EXD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXD3 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			95	5	1	101
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	95	6	1

Variants in EXD3

This is a list of pathogenic ClinVar variants found in the EXD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137306963-C-G		not specified	Uncertain significance (Sep 26, 2022)
9-137306969-G-A		not specified	Uncertain significance (May 16, 2024)
9-137306978-G-A		not specified	Uncertain significance (Jan 17, 2024)
9-137306991-C-T		not specified	Uncertain significance (Dec 12, 2023)
9-137307023-C-T		not specified	Uncertain significance (Dec 06, 2023)
9-137307041-C-T		not specified	Uncertain significance (Sep 14, 2022)
9-137307042-G-A		not specified	Uncertain significance (Jan 26, 2022)
9-137307057-C-T		not specified	Uncertain significance (Feb 10, 2022)
9-137307089-C-T		not specified	Uncertain significance (Dec 15, 2022)
9-137307153-G-A		not specified	Uncertain significance (Jul 13, 2021)
9-137307162-C-T		not specified	Likely benign (Jun 23, 2021)
9-137307167-A-G		not specified	Uncertain significance (Sep 22, 2023)
9-137307622-G-C		not specified	Uncertain significance (Mar 31, 2023)
9-137307641-C-T		not specified	Likely benign (Dec 14, 2022)
9-137309612-C-T		not specified	Uncertain significance (Nov 10, 2022)
9-137309637-T-A		not specified	Uncertain significance (Apr 22, 2024)
9-137309664-C-A		not specified	Uncertain significance (May 04, 2022)
9-137309673-C-A		not specified	Uncertain significance (Jan 23, 2023)
9-137309675-T-C		not specified	Uncertain significance (Mar 01, 2023)
9-137323732-C-T		not specified	Uncertain significance (Feb 28, 2024)
9-137323754-T-C		not specified	Uncertain significance (Feb 07, 2023)
9-137323831-C-T		not specified	Uncertain significance (Sep 15, 2022)
9-137323852-C-G		not specified	Uncertain significance (Jan 31, 2022)
9-137323852-C-T		not specified	Uncertain significance (Jan 03, 2024)
9-137323853-G-A		not specified	Uncertain significance (Jul 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXD3	protein_coding	protein_coding	ENST00000340951	21	116367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.98e-16	0.398	124282	0	151	124433	0.000607

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0412	535	538	0.995	0.0000356	5504
Missense in Polyphen		125	135.22	0.92445		1600
Synonymous	0.328	239	246	0.973	0.0000178	1825
Loss of Function	1.56	30	40.7	0.737	0.00000183	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00212	0.00208
Ashkenazi Jewish	0.000205	0.000199
East Asian	0.00133	0.00128
Finnish	0.000239	0.000186
European (Non-Finnish)	0.000559	0.000542
Middle Eastern	0.00133	0.00128
South Asian	0.000145	0.000131
Other	0.000915	0.000827

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses 3'-5' exoribonuclease activity. Required for 3'-end trimming of AGO1-bound miRNAs (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.895
• rvis_EVS: 2.95
• rvis_percentile_EVS: 99.17

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Gene ontology

• Biological process: nucleic acid phosphodiester bond hydrolysis
• Molecular function: nucleic acid binding;protein binding;3'-5' exonuclease activity;metal ion binding