EML1 p.Arg85=
c.253A>C · rs369479741 · VCV3046559
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00297%, nfe)
Conditions
1
EML1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>G here scores Δ0.88 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 16.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00297%
European (non-Finnish) · 35/1,179,928 alleles
Filtering AF
0.00215%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00191%
Overall
0.00223%
36/1,613,744 alleles · very rare
exomes 34/1,461,560 · genomes 2/152,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00297% | 33,712 |
| Admixed American | 0.00167% | 59,894 |
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.Arg85=
- Coding
- c.253A>C
- MANE Select
- NM_004434
- dbSNP
- rs369479741
- Type
- single nucleotide variant
- Location
- chr14:99865516 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 1 PDB
- Residue 85
- the 'disordered' 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.His317= Likely benign same condition
- EML1 p.Leu466= Likely benign same condition
- EML1 p.Pro242= 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-arg85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown