EML1 p.Thr96=
c.288G>A · rs139087520 · VCV740438
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, 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 -5.7 | GERP -3.1 |
| Overall | ||
| CADD | 6.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,908 alleles
Filtering AF
0.00624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.00149%
24/1,614,010 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.012% | 8,323 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,623 |
| Admixed American | 0.00333% | 29,998 |
| East Asian | 0.00223% | 44,890 |
| South Asian | 0.0022% | 45,540 |
| European (non-Finnish) | 0.000508% | 196,671 |
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.Thr96=
- Coding
- c.288G>A
- MANE Select
- NM_004434
- dbSNP
- rs139087520
- Type
- single nucleotide variant
- Location
- chr14:99865551 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 1 PDB
- Residue 96
- the 'disordered' region
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-thr96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown