Is ATM p.Pro862= (c.2586T>C) pathogenic?

ATM p.Pro862= (c.2586T>C) is classified Benign/Likely benign in ATM (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-05-09). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with ATM p.Pro862= (c.2586T>C)?

ATM p.Pro862= (c.2586T>C) is associated with hereditary neoplastic syndrome, ataxia telangiectasia, hereditary breast carcinoma (ClinVar).

How common is ATM p.Pro862= (c.2586T>C) in the general population?

ATM p.Pro862= (c.2586T>C) is absent from gnomAD v4.1 (gnomAD).

ATM p.Pro862=

c.2586T>C · rs2135508452 · VCV1149054

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

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 carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.62	GERP -3.2, phastCons 0.006
Overall
CADD	2.862	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.Pro862=
Coding: c.2586T>C
MANE Select: NM_000051
dbSNP: rs2135508452
Type: single nucleotide variant
Location: chr11:108267290 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 862: 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 neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ataxia telangiectasia hereditary breast carcinoma

Similar variants

ATM p.Pro862Ala Uncertain significance ★★ ⚠ same residue
ATM p.Pro862Ser Uncertain significance ★★ ⚠ same residue
ATM p.Pro862Arg Uncertain significance ★ ⚠ same residue
ATM p.Pro862His Uncertain significance ★ ⚠ same residue
ATM p.Pro862Thr Likely benign ★ same residue
ATM p.Pro862fs Pathogenic ★★ same residue
ATM c.1607+1G>T Pathogenic ★★★ same condition
ATM c.2251-4A>G 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-pro862 (accessed [today's date]).

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