Is ATM p.Ile665= (c.1995T>A) pathogenic?

ATM p.Ile665= (c.1995T>A) is classified Benign/Likely benign in ATM (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-27). Absent from gnomAD v4.1; Associated with hereditary breast carcinoma.

What condition is associated with ATM p.Ile665= (c.1995T>A)?

ATM p.Ile665= (c.1995T>A) is associated with hereditary breast carcinoma, ataxia telangiectasia (ClinVar).

How common is ATM p.Ile665= (c.1995T>A) in the general population?

ATM p.Ile665= (c.1995T>A) is absent from gnomAD v4.1 (gnomAD).

How is Hereditary breast cancer inherited?

Typically Autosomal dominant, Multigenic/multifactorial (Orphanet). A genetic counselor can assess individual risk for a family.

ATM p.Ile665=

c.1995T>A · rs1555073271 · VCV2771864

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary breast carcinoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.29	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 0.058	GERP -2.9
Overall
CADD	9.65	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.Ile665=
Coding: c.1995T>A
MANE Select: NM_000051
dbSNP: rs1555073271
Type: single nucleotide variant
Location: chr11:108253910 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 665: a UniProt-annotated variant site (in at); a UniProt-annotated variant site (in at; uncertain significance)

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

Disease context

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

Also linked: ataxia telangiectasia

For Hereditary breast cancer (Orphanet):

Inheritance: Autosomal dominant, Multigenic/multifactorial
Onset: Adult, Elderly

Similar variants

ATM p.Ile665Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
ATM p.Ile665Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
ATM p.Ile665Val Conflicting classifications of pathogenicity ★ ⚠ same residue
ATM p.Ile665fs Pathogenic ★★ 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
ATM c.3078-1G>A 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-ile665 (accessed [today's date]).

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