Is ATM p.Ser1655fs (c.4963del) pathogenic?

ATM p.Ser1655fs (c.4963del) is classified Pathogenic in ATM (ClinVar, Single submitter, 1 submitter; last evaluated 2026-05-19). Associated with hereditary neoplastic syndrome.

What condition is associated with ATM p.Ser1655fs (c.4963del)?

ATM p.Ser1655fs (c.4963del) is associated with hereditary neoplastic syndrome (ClinVar).

ATM p.Ser1655fs

c.4963del · VCV4866790

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

hereditary neoplastic syndrome

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 haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 33 of 63
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.92	GERP -3.1, phastCons 0.98

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

Variant & gene context

Gene: ATM
Protein: p.Ser1655fs
Coding: c.4963del
MANE Select: NM_000051
Type: Deletion
Location: chr11:108297340 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 1655: a UniProt-annotated variant site (in at); a UniProt-annotated variant site (in at; uncertain significance); an α-helix; a UniProt-annotated variant site (in at; uncertain significance; increases protein abundance)

Full ATM 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

ATM p.Ser1655Phe Uncertain significance ★★ same residue
ATM p.Ser1655Pro Uncertain significance ★★ same residue
ATM p.Ser1655Tyr Conflicting classifications of pathogenicity ★ same residue
ATM p.Ser1655= Likely benign ★ same residue
ATM c.2639-22_2639-20del Pathogenic ★★★ same condition
ATM p.Asn1719fs Pathogenic ★★★ same condition
ATM p.Asp130fs Pathogenic ★★★ same condition
ATM p.Glu1267_Val1268insTer 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/atm-p-ser1655fs (accessed [today's date]).

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