EGFR p.Leu862=
c.2586G>A · VCV3773447
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
1
lung cancer
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.61 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.34 | gain · loss 0.09 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -5.1 | GERP -3.8 |
| Overall | ||
| CADD | 12.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,086 alleles
Overall
6.84e-05%
1/1,461,784 alleles · very rare
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
- EGFR
- Protein
- p.Leu862=
- Coding
- c.2586G>A
- MANE Select
- NM_005228
- Type
- single nucleotide variant
- Location
- chr7:55191835 (GRCh38)
- Gene constraint
- LOEUF 0.475 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.29 · 393 PDB
- Residue 862
- a turn; the protein kinase domain
Similar variants
- EGFR p.Arg1031Gln Uncertain significance ★★ ⚠ same condition
- EGFR p.Arg165Trp Uncertain significance ★★ ⚠ same condition
- EGFR p.Arg671His Uncertain significance ★★ ⚠ same condition
- EGFR p.Arg831Cys Uncertain significance ★★ ⚠ same condition
- EGFR p.Arg999His Uncertain significance ★★ ⚠ same condition
- EGFR p.Asp1006Ala Uncertain significance ★★ ⚠ same condition
- EGFR p.Asp1012His Uncertain significance ★★ ⚠ same condition
- EGFR p.Gln1159Arg Uncertain significance ★★ ⚠ same condition
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/egfr-p-leu862 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown