EML1 p.Leu484=
c.1452C>T · rs147023936 · VCV754280
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.069%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.035 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP 0.72, phastCons 1 |
| Overall | ||
| CADD | 11.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.069%
European (non-Finnish) · 814/1,179,784 alleles
Filtering AF
0.065%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0635%
Overall
0.0531%
856/1,612,476 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.069% | 1,449 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,469 |
| Finnishnot grpmax-eligible | 0.0203% | 4,924 |
| African / African-American | 0.0107% | 9,351 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,592 |
| Admixed American | 0.00337% | 29,705 |
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.Leu484=
- Coding
- c.1452C>T
- MANE Select
- NM_004434
- dbSNP
- rs147023936
- Type
- single nucleotide variant
- Location
- chr14:99911534 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 1 PDB
- Residue 484
- the 'tandem atypical propeller in emls' region; a β-strand
Similar variants
- EML1 p.Ala292Val Uncertain significance ★★ ⚠ same type
- EML1 p.Arg192His Uncertain significance ★★ ⚠ same type
- EML1 p.Arg450Gln Uncertain significance ★★ ⚠ same type
- EML1 p.Arg813His Uncertain significance ★★ ⚠ same type
- EML1 p.Cys369Phe Uncertain significance ★★ ⚠ same type
- EML1 p.Gln409Glu Uncertain significance ★★ ⚠ same type
- EML1 p.His351Gln Uncertain significance ★★ ⚠ same type
- EML1 p.Val253Met 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-leu484 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown