Is ATM p.Gly1663= (c.4989T>A) pathogenic?

ATM p.Gly1663= (c.4989T>A) is classified Likely benign in ATM (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-12). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with ATM p.Gly1663= (c.4989T>A)?

ATM p.Gly1663= (c.4989T>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is ATM p.Gly1663= (c.4989T>A) in the general population?

ATM p.Gly1663= (c.4989T>A) is absent from gnomAD v4.1 (gnomAD).

ATM p.Gly1663=

c.4989T>A · rs1591693006 · VCV1744557

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/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.24	donor gain, 16 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -1.2	GERP -4.4, phastCons 0.002
Overall
CADD	8.032	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: ATM
Protein: p.Gly1663=
Coding: c.4989T>A
MANE Select: NM_000051
dbSNP: rs1591693006
Type: single nucleotide variant
Location: chr11:108297366 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 1663: a UniProt-annotated variant site (in at); a UniProt-annotated variant site (in at; uncertain significance); a β-strand; 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.Gly1663Asp Uncertain significance ★★ ⚠ same residue
ATM p.Gly1663Ser Uncertain significance ★★ ⚠ same residue
ATM p.Gly1663Ala Uncertain significance ★ ⚠ same residue
ATM p.Gly1663Cys Uncertain significance ★ same residue
ATM p.Gly1663Val Uncertain significance ★ same residue
ATM c.1607+1G>T Pathogenic ★★★ same condition
ATM c.2251-4A>G Likely pathogenic ★★★ same condition
ATM c.2466+5G>C 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/atm-p-gly1663 (accessed [today's date]).

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