Is ATM p.Pro2029= (c.6087C>T) pathogenic?

ATM p.Pro2029= (c.6087C>T) is classified Benign/Likely benign in ATM (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-12-20). Very rare (popmax 0.00446%, eas); Associated with hereditary neoplastic syndrome.

What condition is associated with ATM p.Pro2029= (c.6087C>T)?

ATM p.Pro2029= (c.6087C>T) is associated with hereditary neoplastic syndrome, ataxia telangiectasia, hereditary breast carcinoma (ClinVar).

How common is ATM p.Pro2029= (c.6087C>T) in the general population?

ATM p.Pro2029= (c.6087C>T) is very rare (popmax 0.00446%, eas) (gnomAD).

ATM p.Pro2029=

c.6087C>T · rs1060504316 · VCV414618

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

Conditions

hereditary neoplastic syndrome

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.1	GERP -2.1
Overall
CADD	3.648	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,856 alleles

Filtering AF 0.000739% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000277%

Overall 0.000372% 6/1,610,802 alleles · very rare exomes 6/1,458,622 · genomes 0/152,180 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00446%	22,428
Finnishnot grpmax-eligible	0.00156%	63,992
European (non-Finnish)	0.000255%	392,369

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.Pro2029=
Coding: c.6087C>T
MANE Select: NM_000051
dbSNP: rs1060504316
Type: single nucleotide variant
Location: chr11:108315903 (GRCh38)

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

Also linked: ataxia telangiectasia hereditary breast carcinoma

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-pro2029 (accessed [today's date]).

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