Is EGFR p.Pro1090Ser (c.3268C>T) pathogenic?

EGFR p.Pro1090Ser (c.3268C>T) is classified Uncertain significance in EGFR (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-18). AlphaMissense: likely benign (0.1526); Very rare (popmax 0.0017%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with EGFR p.Pro1090Ser (c.3268C>T)?

EGFR p.Pro1090Ser (c.3268C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is EGFR p.Pro1090Ser (c.3268C>T) in the general population?

EGFR p.Pro1090Ser (c.3268C>T) is very rare (popmax 0.0017%, nfe) (gnomAD).

What do computational predictors say about EGFR p.Pro1090Ser (c.3268C>T)?

AlphaMissense predicts likely benign (score 0.1526) — an in-silico prediction, not a clinical call.

EGFR p.Pro1090Ser

c.3268C>T · rs367870311 · VCV965676

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.1526 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0017%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1526	likely benign
REVEL	0.258	benign-leaning
SaProt	LLR -6.52	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 1.7, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 5,238 bp · p 0.97 · regional, not allelic
Overall
CADD	23.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0017% European (non-Finnish) · 20/1,178,688 alleles

Filtering AF 0.00111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000901%

Overall 0.00124% 20/1,611,204 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.Pro1090Ser
Coding: c.3268C>T
MANE Select: NM_005228
dbSNP: rs367870311
Type: single nucleotide variant
Location: chr7:55202622 (GRCh38)
Gene constraint: LOEUF 0.475 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 76.29 · 393 PDB

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EGFR p.Pro1090= Conflicting classifications of pathogenicity ★ same residue
EGFR p.Pro1090Leu Uncertain significance ★ ⚠ same residue
EGFR p.Pro1090Ala Uncertain significance ★ ⚠ same residue
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
EGFR c.1499-3C>T 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-pro1090ser (accessed [today's date]).

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