Is ATM p.Pro1069= (c.3207T>C) pathogenic?

ATM p.Pro1069= (c.3207T>C) is classified Likely benign in ATM (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-29). Very rare (popmax 8.47e-05%, nfe); Associated with ataxia telangiectasia.

What condition is associated with ATM p.Pro1069= (c.3207T>C)?

ATM p.Pro1069= (c.3207T>C) is associated with ataxia telangiectasia (ClinVar).

How common is ATM p.Pro1069= (c.3207T>C) in the general population?

ATM p.Pro1069= (c.3207T>C) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is Ataxia-telangiectasia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ATM p.Pro1069=

c.3207T>C · rs878853502 · VCV236702

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

ataxia telangiectasia

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 -0.06	GERP 0.14, phastCons 0.89
Overall
CADD	6.847	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,006 alleles

Overall 6.84e-05% 1/1,461,782 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ATM
Protein: p.Pro1069=
Coding: c.3207T>C
MANE Select: NM_000051
dbSNP: rs878853502
Type: single nucleotide variant
Location: chr11:108272775 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 1069: a UniProt-annotated variant site (in at); a β-strand; 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

ataxia telangiectasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Ataxia-telangiectasia (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy
Prevalence: 1-5 / 10 000 (Norway)

Similar variants

ATM p.Pro1069Ala Uncertain significance ★★ ⚠ same residue
ATM p.Pro1069Leu Uncertain significance ★ same residue
ATM p.Pro1069Thr Uncertain significance ★ ⚠ same residue
ATM p.Pro1069fs Pathogenic/Likely pathogenic ★★ same residue
ATM p.Pro1069Ser Likely benign ★ 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-pro1069 (accessed [today's date]).

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