Is EGFR p.Ala147fs (c.439del) pathogenic?

EGFR p.Ala147fs (c.439del) is classified Pathogenic in EGFR (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-09). Absent from gnomAD; Associated with EGFR-related lung cancer.

What condition is associated with EGFR p.Ala147fs (c.439del)?

EGFR p.Ala147fs (c.439del) is associated with EGFR-related lung cancer (ClinVar).

How common is EGFR p.Ala147fs (c.439del) in the general population?

EGFR p.Ala147fs (c.439del) is absent from gnomAD (gnomAD).

EGFR p.Ala147fs

c.439del · rs2535465944 · VCV2844629

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

EGFR-related lung cancer

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 4 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -7.6	GERP -4.2

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EGFR
Protein: p.Ala147fs
Coding: c.439del
MANE Select: NM_005228
dbSNP: rs2535465944
Type: Deletion
Location: chr7:55146620 (GRCh38)
Gene constraint: LOEUF 0.475 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 76.29 · 393 PDB
Residue 147: a β-strand; a UniProt-annotated variant site (variant egfr viii; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed)

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

Disease context

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

Similar variants

EGFR p.Ala147Ser Uncertain significance ★ ⚠ same residue
EGFR p.Ala147Val Uncertain significance ★ ⚠ same residue
EGFR p.Ala147= Likely benign ★ same residue
EGFR p.Ala147Pro Uncertain significance ★★ ⚠ same residue
EGFR p.Ala147Thr Uncertain significance ★★ ⚠ same residue
EGFR p.Leu12_Leu18del Uncertain significance ★★ same condition
EGFR c.2181_2184+7del Likely pathogenic ★ same condition
EGFR c.2555_2626-421del Likely pathogenic ★ 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-ala147fs (accessed [today's date]).

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