ENDOD1

protein-coding

endonuclease domain containing 1

Gene summary

Predicted to enable several functions, including endonuclease activity; metal ion binding activity; and nucleic acid binding activity. Predicted to be involved in innate immune response. Located in extracellular exosome and membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015036.3

Inheritance

—

ClinVar variants

U:72B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.08

Max pathogenic AF

—

Genomic locus

chr11:95,089,846-95,132,645

External References & Databases

Ensembl (ENSG00000149218)

Transcript & Mutation Effects

hg38 • Region Span ~42.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ENDOD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015036.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			72 clinvar	7 clinvar		79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	9	0	81

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015036.3	RefSeq	NP_055851.1	2	MANE Select
ENST00000278505.5	Ensembl	ENSP00000278505.4	2	MANE Select
ENST00000878168.1	Ensembl	ENSP00000548227.1	3	Standard
ENST00000878168.2	Ensembl	ENSP00000548227.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Platelet degranulation
Response to elevated platelet cytosolic Ca2+
Platelet activation, signaling and aggregation
Hemostasis

Biological Process

platelet degranulation
nucleic acid phosphodiester bond hydrolysis

Molecular Function

nucleic acid binding
endonuclease activity
metal ion binding

Cellular Component

extracellular region
cytosol
membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000278505
Coding exons: 2
Length: 42836
Individuals with no LoFs: 124735
Homozygous LoFs: 0
Heterozygous LoFs: 61
Defined: 124796
p: 0.000244

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0100	259	259	0.998	0.0000130	3227
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00038	0.00037	rare
South Asian	0.00013	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a DNase and a RNase. {ECO:0000305}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.713
RVIS EVS: 1
RVIS percentile EVS: 90.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.578

Gene Damage Prediction

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