EML1 p.Pro242=
c.726G>A · rs368509823 · VCV3052796
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0112%, eas)
Conditions
1
EML1-related disorder
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 -5.1 | GERP -3.8 |
| Overall | ||
| CADD | 6.283 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0112%
East Asian · 5/44,766 alleles
Filtering AF
0.00623%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00657%
106/1,612,858 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0112% | 8,953 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,408 |
| European (non-Finnish) | 0.00755% | 13,253 |
| South Asian | 0.0033% | 30,270 |
| Finnishnot grpmax-eligible | 0.00312% | 32,012 |
| African / African-American | 0.00133% | 74,936 |
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
- EML1
- Protein
- p.Pro242=
- Coding
- c.726G>A
- MANE Select
- NM_004434
- dbSNP
- rs368509823
- Type
- single nucleotide variant
- Location
- chr14:99897193 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 1 PDB
- Residue 242
- the 'tandem atypical propeller in emls' region
Disease context
EML1-related disorder
Similar variants
- EML1 c.519-9T>C Likely benign same condition
- EML1 c.67+6G>C Likely benign same condition
- EML1 p.Arg85= Likely benign same condition
- EML1 p.His317= Likely benign same condition
- EML1 p.Leu466= Likely benign same condition
- EML1 p.Ala292Val Uncertain significance ★★ ⚠ same type
- EML1 p.Arg192His Uncertain significance ★★ ⚠ same type
- EML1 p.Arg450Gln 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/eml1-p-pro242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown