EPB41 p.Ser85=
c.255G>A · rs375223119 · VCV3046789
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.048%, 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 -1.9 | GERP -5.2 |
| Overall | ||
| CADD | 4.547 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.048%
African / African-American · 36/75,034 alleles
Filtering AF
0.0356%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0313%
Overall
0.00341%
55/1,614,174 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.048% | 2,084 |
| Admixed American | 0.0133% | 7,502 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
| East Asian | 0.00223% | 44,882 |
| South Asian | 0.0022% | 45,540 |
| European (non-Finnish) | 0.000424% | 236,008 |
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
- EPB41
- Protein
- p.Ser85=
- Coding
- c.255G>A
- MANE Select
- NM_001376013
- dbSNP
- rs375223119
- Type
- single nucleotide variant
- Location
- chr1:28987692 (GRCh38)
- Gene constraint
- LOEUF 0.738 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.72 · 3 PDB
- Residue 85
- the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- EPB41 p.Arg471Ter Pathogenic/Likely pathogenic ★★ same type
- EPB41 p.Arg508Ter Pathogenic/Likely pathogenic ★★ same type
- EPB41 p.Arg554Ter Pathogenic/Likely pathogenic ★★ same type
- EPB41 p.Arg715Ter Pathogenic ★★ same type
- EPB41 p.Gln274Ter Pathogenic ★★ same type
- EPB41 p.Met210Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- EPB41 p.Tyr331Ter Pathogenic/Likely pathogenic ★★ same type
- EPB41 p.Ala259Val 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/epb41-p-ser85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown