EPB41L3

Chr 18

erythrocyte membrane protein band 4.1 like 3

Also known as: 4.1B, DAL-1, DAL1

NCBI Gene: 23136ENSG00000082397UniProt: Q9Y2J2

Predicted to enable cytoskeletal protein-membrane anchor activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in several processes, including nervous system development; paranodal junction maintenance; and protein localization to axon. Located in several cellular components, including cell-cell junction; ciliary basal body; and cytosol. Implicated in esophagus squamous cell carcinoma. Biomarker of meningioma. [provided by Alliance of Genome Resources, Jul 2025]

Research Assistant →
0
Active trials
8
Pubs (1 yr)
3
P/LP submissions
0%
P/LP missense
0.48
LOEUF
LOF
Mechanism· G2P
Clinical Summary— EPB41L3
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.33) despite low pLI — interpret in context.
📋
ClinVar Variants
3 unique Pathogenic / Likely Pathogenic· 73 VUS of 100 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.48LOEUF
pLI 0.000
Z-score 4.78
OE 0.33 (0.23–0.48)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.48Z-score
OE missense 0.84 (0.78–0.90)
534 obs / 639.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.33 (0.23–0.48)
0≤0.351.4
Missense OE0.84 (0.78–0.90)
0≤0.61.4
Synonymous OE1.04
0≤1.21.6
LoF obs/exp: 19 / 58.5Missense obs/exp: 534 / 639.3Syn Z: -0.52
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
moderateEPB41L3-related developmental disorder with delayed myelination and seizuresLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.7229th %ile
GOF
0.76top 25%
LOF
0.3940th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

100 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic2
Likely Pathogenic1
VUS73
Likely Benign3
2
Pathogenic
1
Likely Pathogenic
73
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
2
0
2
Likely Pathogenic
0
0
1
0
1
VUS
0
71
2
0
73
Likely Benign
0
3
0
0
3
Benign
0
0
0
0
0
Total0745079

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

View in ClinVar →

Protein Context — Lollipop Plot

EPB41L3 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients