EEPD1

endonuclease/exonuclease/phosphatase family domain containing 1

Basic information

Region (hg38): 7:36153254-36301538

Links

ENSG00000122547 ∙ NCBI:80820 ∙ OMIM:617192 ∙ HGNC:22223 ∙ Uniprot:Q7L9B9 ∙ 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 EEPD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEPD1 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			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	0

Variants in EEPD1

This is a list of pathogenic ClinVar variants found in the EEPD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-36154383-A-G		not specified	Uncertain significance (Dec 20, 2022)
7-36154419-A-G		not specified	Uncertain significance (Dec 13, 2022)
7-36154454-A-G		not specified	Uncertain significance (Aug 11, 2022)
7-36154494-C-T		not specified	Uncertain significance (Oct 16, 2023)
7-36154580-G-A		not specified	Uncertain significance (Sep 16, 2021)
7-36154629-G-T		not specified	Uncertain significance (Apr 06, 2023)
7-36154637-A-G		not specified	Uncertain significance (Apr 12, 2022)
7-36154653-C-T		not specified	Uncertain significance (Jan 16, 2024)
7-36154683-C-G		not specified	Uncertain significance (Jul 12, 2022)
7-36154713-C-T		not specified	Uncertain significance (Aug 12, 2021)
7-36154766-A-G		not specified	Uncertain significance (Sep 22, 2023)
7-36154779-G-A		not specified	Uncertain significance (Sep 12, 2023)
7-36154799-C-G		not specified	Likely benign (Jul 14, 2021)
7-36154857-T-C		not specified	Uncertain significance (Mar 16, 2024)
7-36154875-A-G		not specified	Uncertain significance (Jul 06, 2021)
7-36154880-G-A		not specified	Uncertain significance (May 17, 2023)
7-36154964-A-G		not specified	Uncertain significance (May 16, 2024)
7-36155155-C-A		not specified	Uncertain significance (Jun 29, 2023)
7-36155169-G-A		not specified	Uncertain significance (May 24, 2023)
7-36281136-C-G		not specified	Uncertain significance (Nov 14, 2023)
7-36281137-C-T		not specified	Uncertain significance (Jan 03, 2024)
7-36281190-G-A		not specified	Uncertain significance (Sep 17, 2021)
7-36284690-C-T		not specified	Uncertain significance (Jul 12, 2023)
7-36284713-G-A		not specified	Uncertain significance (May 02, 2024)
7-36284717-C-T		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEPD1	protein_coding	protein_coding	ENST00000242108	7	148395

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0549	0.944	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	284	354	0.801	0.0000223	3710
Missense in Polyphen		77	115.42	0.66711		1141
Synonymous	0.972	144	160	0.902	0.0000109	1174
Loss of Function	2.95	6	20.4	0.294	0.00000112	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.000114	0.000109
South Asian	0.0000668	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.161
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.15

Haploinsufficiency Scores

• pHI: 0.241
• hipred: N
• hipred_score: 0.475
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.358

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eepd1

Zebrafish Information Network

• Gene name: eepd1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: DNA repair
• Molecular function: DNA binding