EPDR1

Chr 7

ependymin related 1

Also known as: EPDR, MERP-1, MERP1, UCC1

NCBI Gene: 54749ENSG00000086289UniProt: Q9UM22

The protein encoded by this gene is a type II transmembrane protein that is similar to two families of cell adhesion molecules, the protocadherins and ependymins. This protein may play a role in calcium-dependent cell adhesion. This protein is glycosylated, and the orthologous mouse protein is localized to the lysosome. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 8. [provided by RefSeq, Aug 2011]

54
ClinVar variants
19
Pathogenic / LP
0.02
pLI score
0
Active trials
Clinical Summary— EPDR1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.02) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
19 Pathogenic / Likely Pathogenic· 34 VUS of 54 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.05LOEUF
pLI 0.018
Z-score 1.48
OE 0.46 (0.23–1.05)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.41Z-score
OE missense 1.10 (0.96–1.28)
132 obs / 119.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.46 (0.23–1.05)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.10 (0.96–1.28)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.02
0≤1.21.6
LoF obs/exp: 4 / 8.7Missense obs/exp: 132 / 119.5Syn Z: -0.11

ClinVar Variant Classifications

54 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic16
Likely Pathogenic3
VUS34
Likely Benign1
16
Pathogenic
3
Likely Pathogenic
34
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
16
0
16
Likely Pathogenic
0
0
3
0
3
VUS
0
31
3
0
34
Likely Benign
0
1
0
0
1
Benign
0
0
0
0
0
Total03222054

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

EPDR1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
EPDR1 promotes PD-L1 expression and tumor immune evasion by inhibiting TRIM21-dependent ubiquitylation of IkappaB kinase-β.
Qian X et al.·EMBO J
2024
A mechanistic framework for cardiometabolic and coronary artery diseases.
Koplev S et al.·Nat Cardiovasc Res
2022
Major Genetic Risk Factors for Dupuytren's Disease Are Inherited From Neandertals.
Ågren R et al.·Mol Biol Evol
2023
Identification of bone mineral density associated genes with shared genetic architectures across multiple tissues: Functional insights for EPDR1, PKDCC, and SPTBN1.
Jung J et al.·PLoS One
2024Functional
Genome-Wide Interaction Study of Dietary Intake and Colorectal Cancer Risk in the UK Biobank.
Hoang T et al.·JAMA Netw Open
2024
A Genome-Wide Association Study and Rare Variant Analysis for Dupuytren Disease in a North American Population.
Grandizio LC et al.·J Hand Surg Am
2025
Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density.
Chesi A et al.·Nat Commun
2019
First reported case of fragile foal syndrome type 1 in the Thoroughbred caused by PLOD1 c.2032G>A.
Grillos AS et al.·Equine Vet J
2022Case report
Evaluation of the association between five genetic variants and primary open-angle glaucoma in a Han Chinese population.
Li K et al.·Ophthalmic Genet
2020
Genetic characterization of vocal fold lesions: leukoplakia and carcinoma.
Bartlett RS et al.·Laryngoscope
2012
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools