EML1 p.Ser488=
c.1464C>T · rs553247254 · VCV792340
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0135%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.297 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.1 | GERP -3.2 |
| Overall | ||
| CADD | 5.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0135%
Admixed American · 8/59,310 alleles
Filtering AF
0.00668%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00487%
Overall
0.00205%
33/1,612,098 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0135% | 7,414 |
| South Asian | 0.00773% | 12,935 |
| East Asian | 0.0067% | 14,920 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,226 |
| African / African-American | 0.00134% | 74,890 |
| European (non-Finnish) | 0.00102% | 98,299 |
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.Ser488=
- Coding
- c.1464C>T
- MANE Select
- NM_004434
- dbSNP
- rs553247254
- Type
- single nucleotide variant
- Location
- chr14:99911546 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 1 PDB
- Residue 488
- the 'tandem atypical propeller in emls' 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-ser488 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown