EPDR1

ependymin related 1

Basic information

Region (hg38): 7:37920640-37951936

Links

ENSG00000086289 ∙ NCBI:54749 ∙ OMIM:619734 ∙ HGNC:17572 ∙ Uniprot:Q9UM22 ∙ 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 EPDR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPDR1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in EPDR1

This is a list of pathogenic ClinVar variants found in the EPDR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-37920952-G-T		not specified	Uncertain significance (Feb 05, 2024)
7-37920995-T-C		not specified	Uncertain significance (Feb 03, 2023)
7-37921055-C-A		not specified	Uncertain significance (Dec 14, 2021)
7-37921078-C-A		not specified	Uncertain significance (Jun 06, 2023)
7-37921118-G-C		not specified	Uncertain significance (Jul 20, 2021)
7-37921158-C-G		not specified	Uncertain significance (Mar 25, 2024)
7-37921162-C-A		not specified	Uncertain significance (May 20, 2024)
7-37948890-A-G		not specified	Uncertain significance (Oct 26, 2021)
7-37948931-C-A		not specified	Uncertain significance (Jan 07, 2022)
7-37948932-C-T		not specified	Uncertain significance (Oct 21, 2021)
7-37948976-C-G		not specified	Uncertain significance (Aug 20, 2024)
7-37948986-T-C		not specified	Uncertain significance (Aug 18, 2023)
7-37949003-C-A		not specified	Uncertain significance (Nov 21, 2024)
7-37949025-C-T		not specified	Uncertain significance (May 13, 2024)
7-37950239-A-G		not specified	Uncertain significance (Feb 05, 2024)
7-37950248-A-C		not specified	Uncertain significance (Oct 26, 2021)
7-37950289-C-T		not specified	Uncertain significance (Oct 28, 2023)
7-37950290-G-A		not specified	Uncertain significance (Nov 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPDR1	protein_coding	protein_coding	ENST00000199448	3	268098

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0179	0.902	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.406	132	120	1.10	0.00000582	1428
Missense in Polyphen		36	32.546	1.1061		381
Synonymous	-0.110	51	50.0	1.02	0.00000275	427
Loss of Function	1.48	4	8.70	0.460	3.70e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000375	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.278
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0487

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epdr1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: cell-matrix adhesion
• Cellular component: extracellular region
• Molecular function: calcium ion binding