EPB41L4A p.Pro103=
c.309A>G · rs745648092 · VCV2655633
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -1.6, phastCons 0.001 |
| Overall | ||
| CADD | 8.957 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
African / African-American · 1/73,552 alleles
Filtering AF
0.000189%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000124%
Overall
0.00045%
7/1,556,096 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00136% | 73,552 |
| European (non-Finnish) | 0.000525% | 190,656 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- EPB41L4A
- Protein
- p.Pro103=
- Coding
- c.309A>G
- MANE Select
- NM_022140
- dbSNP
- rs745648092
- Type
- single nucleotide variant
- Location
- chr5:112275352 (GRCh38)
- Gene constraint
- LOEUF 1.261 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.14
- Residue 103
- the ferm domain
Similar variants
- EPB41L4A p.Ser652Arg Uncertain significance ★★ same type
- EPB41L4A p.Thr620Ala Uncertain significance ★★ ⚠ same type
- EPB41L4A p.Tyr90Cys Uncertain significance ★★ ⚠ same type
- EPB41L4A c.1933-9A>G Likely benign ★★ same type
- EPB41L4A p.Lys435Glu Likely benign ★★ same type
- EPB41L4A p.Thr293= Benign/Likely benign ★★ same type
- EPB41L4A p.Ala157Glu Uncertain significance ★ ⚠ same type
- EPB41L4A p.Arg127Cys Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/epb41l4a-p-pro103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown