EXD1

exonuclease 3'-5' domain containing 1

Basic information

Region (hg38): 15:41182725-41230757

Previous symbols: [ "EXDL1" ]

Links

ENSG00000178997 ∙ NCBI:161829 ∙ ∙ HGNC:28507 ∙ Uniprot:Q8NHP7 ∙ 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 EXD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXD1 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			31	1		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	32	1	0

Variants in EXD1

This is a list of pathogenic ClinVar variants found in the EXD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-41183970-C-A		not specified	Uncertain significance (Jan 29, 2024)
15-41183980-G-C		not specified	Uncertain significance (Apr 18, 2023)
15-41184047-C-T		not specified	Likely benign (Oct 01, 2024)
15-41184074-T-C		not specified	Likely benign (Jun 27, 2023)
15-41184089-T-C		not specified	Uncertain significance (Oct 04, 2022)
15-41184134-C-T		not specified	Uncertain significance (Jan 04, 2024)
15-41184138-C-A		not specified	Uncertain significance (May 10, 2024)
15-41184169-T-A		not specified	Uncertain significance (Jul 27, 2024)
15-41184272-C-T		not specified	Uncertain significance (Oct 26, 2022)
15-41184406-C-G		not specified	Uncertain significance (Dec 20, 2023)
15-41184418-C-G		not specified	Uncertain significance (Aug 28, 2024)
15-41184472-A-G		not specified	Uncertain significance (Jan 04, 2024)
15-41184539-G-C		not specified	Uncertain significance (May 12, 2024)
15-41184546-G-C		not specified	Uncertain significance (Jan 30, 2024)
15-41189941-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-41189951-G-A		not specified	Uncertain significance (Jul 05, 2022)
15-41189953-C-T		not specified	Uncertain significance (Jul 30, 2024)
15-41189971-C-T		not specified	Uncertain significance (Nov 17, 2023)
15-41189972-G-A		not specified	Uncertain significance (Oct 12, 2024)
15-41189996-C-T		not specified	Uncertain significance (Jan 31, 2024)
15-41190041-G-A		not specified	Uncertain significance (Aug 30, 2022)
15-41190065-C-T		not specified	Uncertain significance (Dec 13, 2022)
15-41190070-G-A		not specified	Uncertain significance (Aug 30, 2021)
15-41190103-C-T		not specified	Uncertain significance (Apr 22, 2022)
15-41190116-C-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXD1	protein_coding	protein_coding	ENST00000314992	10	48019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.40e-14	0.0595	125623	0	124	125747	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.112	267	262	1.02	0.0000130	3363
Missense in Polyphen		80	76.051	1.0519		929
Synonymous	-0.0775	97	96.0	1.01	0.00000466	982
Loss of Function	0.534	22	24.9	0.884	0.00000126	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000839	0.000837
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000544	0.000544
Finnish	0.00107	0.00102
European (Non-Finnish)	0.000336	0.000334
Middle Eastern	0.000544	0.000544
South Asian	0.00100	0.000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding component of the PET complex, a multiprotein complex required for the processing of piRNAs during spermatogenesis. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposable elements, preventing their mobilization, which is essential for the germline integrity (By similarity). The PET complex is required during the secondary piRNAs metabolic process for the PIWIL2 slicing- triggered loading of PIWIL4 piRNAs. In the PET complex, EXD1 probably acts as an RNA adapter. EXD1 is an inactive exonuclease (By similarity). {ECO:0000250|UniProtKB:H9IUR0, ECO:0000250|UniProtKB:Q8CDF7}.

Intolerance Scores

• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.153
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exd1
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: gene silencing by RNA;piRNA metabolic process;meiotic cell cycle;nucleic acid phosphodiester bond hydrolysis
• Cellular component: P granule;PET complex
• Molecular function: RNA binding;protein binding;3'-5' exonuclease activity;protein homodimerization activity