Is ATM p.Phe802Val (c.2404T>G) pathogenic?

ATM p.Phe802Val (c.2404T>G) is classified Uncertain significance in ATM (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-27). AlphaMissense: likely benign (0.1221); Very rare (popmax 6.2e-05%); Associated with hereditary neoplastic syndrome.

What condition is associated with ATM p.Phe802Val (c.2404T>G)?

ATM p.Phe802Val (c.2404T>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is ATM p.Phe802Val (c.2404T>G) in the general population?

ATM p.Phe802Val (c.2404T>G) is very rare (popmax 6.2e-05%) (gnomAD).

What do computational predictors say about ATM p.Phe802Val (c.2404T>G)?

AlphaMissense predicts likely benign (score 0.1221) — an in-silico prediction, not a clinical call.

ATM p.Phe802Val

c.2404T>G · rs2080695065 · VCV2529892

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1221 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 6.2e-05%)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1221	likely benign
REVEL	0.323	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.4	GERP -1.6, phastCons 0.97
Regional constraint	o/e 0.99	unconstrained · MANE · 66 kb · p 0.75 · regional, not allelic
Overall
CADD	17.05	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.2e-05%

Overall 6.2e-05% 1/1,613,732 alleles · very rare exomes 1/1,461,368 · genomes 0/152,364 · joint denominator

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.Phe802Val
Coding: c.2404T>G
MANE Select: NM_000051
dbSNP: rs2080695065
Type: single nucleotide variant
Location: chr11:108259013 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 802: a UniProt-annotated variant site (in at); an α-helix; 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

Similar variants

ATM p.Phe802Leu Uncertain significance ★★ same residue
ATM p.Phe802= Benign/Likely benign ★★ same residue
ATM p.Phe802Ile 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
ATM c.3078-1G>A Pathogenic ★★★ same condition
ATM c.332-1G>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-phe802val (accessed [today's date]).

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