ENDOD1

endonuclease domain containing 1

Basic information

Region (hg38): 11:95089846-95132645

Links

ENSG00000149218 ∙ NCBI:23052 ∙ OMIM:619568 ∙ HGNC:29129 ∙ Uniprot:O94919 ∙ 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 ENDOD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENDOD1 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				2		2
missense			26	4		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	6	0

Variants in ENDOD1

This is a list of pathogenic ClinVar variants found in the ENDOD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-95089944-G-C		not specified	Uncertain significance (Aug 11, 2022)
11-95089961-C-T		not specified	Uncertain significance (Jun 10, 2024)
11-95090031-A-T		not specified	Uncertain significance (Nov 16, 2021)
11-95090060-G-T		not specified	Uncertain significance (Oct 05, 2023)
11-95090063-G-A		not specified	Uncertain significance (May 07, 2024)
11-95090157-T-G		not specified	Uncertain significance (Sep 17, 2021)
11-95090165-G-A		not specified	Uncertain significance (Nov 17, 2022)
11-95090174-G-T		not specified	Uncertain significance (May 17, 2023)
11-95090180-C-T		not specified	Uncertain significance (Sep 22, 2022)
11-95090195-G-T		not specified	Uncertain significance (Oct 12, 2021)
11-95128454-C-A		not specified	Uncertain significance (Oct 12, 2022)
11-95128472-A-G			Likely benign (Jan 01, 2023)
11-95128593-C-T		not specified	Uncertain significance (Nov 09, 2022)
11-95128623-G-A		not specified	Uncertain significance (Feb 06, 2024)
11-95128682-A-G			Likely benign (Jan 01, 2023)
11-95128704-A-G		not specified	Uncertain significance (Dec 01, 2022)
11-95128710-A-G		not specified	Uncertain significance (Feb 16, 2023)
11-95128764-G-A		not specified	Uncertain significance (Apr 04, 2024)
11-95128786-T-A		not specified	Uncertain significance (Jun 21, 2022)
11-95128797-C-T		not specified	Uncertain significance (Jan 31, 2024)
11-95128798-G-A		not specified	Likely benign (May 24, 2023)
11-95128902-A-C		not specified	Uncertain significance (Dec 12, 2023)
11-95128912-T-C		not specified	Uncertain significance (Oct 03, 2022)
11-95128927-A-C		not specified	Uncertain significance (Oct 17, 2023)
11-95128945-A-G		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENDOD1	protein_coding	protein_coding	ENST00000278505	2	42836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.58e-11	0.0363	124735	0	61	124796	0.000244

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0100	259	259	0.998	0.0000130	3227
Missense in Polyphen		78	85.164	0.91588		1077
Synonymous	-0.411	108	103	1.05	0.00000483	1046
Loss of Function	-0.281	15	13.9	1.08	7.73e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000305
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000379	0.000371
Middle Eastern	0.000223	0.000223
South Asian	0.000131	0.000131
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a DNase and a RNase. {ECO:0000305}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.713
• rvis_EVS: 1
• rvis_percentile_EVS: 90.62

Haploinsufficiency Scores

• pHI: 0.234
• hipred: N
• hipred_score: 0.170
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.578

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Endod1

Gene ontology

• Biological process: platelet degranulation;nucleic acid phosphodiester bond hydrolysis
• Cellular component: extracellular region;cytosol;membrane;extracellular exosome
• Molecular function: nucleic acid binding;endonuclease activity;metal ion binding