Is EGFR p.Arg962= (c.2886T>C) pathogenic?

EGFR p.Arg962= (c.2886T>C) is classified Likely benign in EGFR (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-02). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with EGFR p.Arg962= (c.2886T>C)?

EGFR p.Arg962= (c.2886T>C) is associated with hereditary neoplastic syndrome (ClinVar).

How common is EGFR p.Arg962= (c.2886T>C) in the general population?

EGFR p.Arg962= (c.2886T>C) is absent from gnomAD v4.1 (gnomAD).

EGFR p.Arg962=

c.2886T>C · VCV4247331

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

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 -8.8	GERP -3.8
Overall
CADD	1.105	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EGFR
Protein: p.Arg962=
Coding: c.2886T>C
MANE Select: NM_005228
Type: single nucleotide variant
Location: chr7:55200353 (GRCh38)
Gene constraint: LOEUF 0.475 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 76.29 · 393 PDB
Residue 962: a UniProt-annotated variant site (in); an α-helix; the protein kinase domain

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.Arg962Cys Uncertain significance ★★ same residue
EGFR p.Arg962Gly Uncertain significance ★★ ⚠ same residue
EGFR p.Arg962His Conflicting classifications of pathogenicity ★ ⚠ same residue
EGFR p.Arg962_Glu963insSer Uncertain significance ★ same residue
EGFR p.Arg962Ser 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

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-arg962 (accessed [today's date]).

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