Is EGFR p.Gln787= (c.2361G>A) pathogenic?

EGFR p.Gln787= (c.2361G>A) is classified Benign in EGFR (ClinVar, Multiple submitters, 13 submitters; last evaluated 2026-02-04). Common (popmax 61.4%, mid) — too common for a highly-penetrant pathogenic allele; Associated with lung cancer.

What condition is associated with EGFR p.Gln787= (c.2361G>A)?

EGFR p.Gln787= (c.2361G>A) is associated with lung cancer, squamous cell lung carcinoma, lung carcinoma (ClinVar).

EGFR p.Gln787=

Q: How common is EGFR p.Gln787= (c.2361G>A) in the general population?

EGFR p.Gln787= (c.2361G>A) is common (popmax 61.4%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2361G>A · rs1050171 · VCV45271

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 13 submitters

gnomAD v4.1

Common

common (popmax 61.4%, mid) — too common for a highly-penetrant pathogenic allele

Conditions

lung cancer

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 2.9	GERP 1.8, phastCons 1
Overall
CADD	17.72	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 61.4% Middle Eastern · 3,718/6,060 alleles

Filtering AF 59.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 59%

Overall 55.8% 900,702/1,613,948 alleles · common

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	66.6%	2
Middle Easterngrpmax	61.4%	2
European (non-Finnish)	58.9%	2
Amishnot grpmax-eligible	57%	2
Admixed American	55.6%	2
Remaining individualsnot grpmax-eligible	55%	2
South Asian	50.6%	2
Finnishnot grpmax-eligible	46.9%	2
African / African-American	40.7%	2
East Asian	16.3%	6

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Gln787=
Coding: c.2361G>A
MANE Select: NM_005228
dbSNP: rs1050171
Type: single nucleotide variant
Location: chr7:55181370 (GRCh38)
Gene constraint: LOEUF 0.475 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 76.29 · 393 PDB
Residue 787: a UniProt-annotated variant site (found in a lung cancer sample); a β-strand; the protein kinase domain

Full EGFR gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

lung cancer — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: squamous cell lung carcinoma lung carcinoma inflammatory skin and bowel disease, neonatal, 2 hereditary neoplastic syndrome

Similar variants

EGFR p.Gln787del Uncertain significance ★ same residue
EGFR p.Gln787_Leu788= Benign ★ same residue
EGFR p.Gln787His Uncertain significance ★ ⚠ same residue
EGFR p.Gly428Asp Pathogenic ★★ same condition
EGFR c.1207+5G>A Uncertain significance ★★ same condition
EGFR c.1298+3A>G Uncertain significance ★★ same condition
EGFR c.1298+4A>G Uncertain significance ★★ same condition
EGFR c.1298+6T>C 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-gln787 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown