ATM p.Phe657fs
c.1968_1977del · VCV3653075
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
ataxia telangiectasia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 13 of 63 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 2.6, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ATM
- Protein
- p.Phe657fs
- Coding
- c.1968_1977del
- MANE Select
- NM_000051
- Type
- Deletion
- Location
- chr11:108253883 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Residue 657
- a UniProt-annotated variant site (in at); a UniProt-annotated variant site (in at; uncertain significance)
Disease context
ataxia telangiectasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Ataxia-telangiectasia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy
- Prevalence
- 1-5 / 10 000 (Norway)
Similar variants
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- ATM p.Asn1719fs Pathogenic ★★★ same condition
- ATM p.Asp130fs Pathogenic ★★★ same condition
- ATM p.Glu1267_Val1268insTer Pathogenic ★★★ same condition
- ATM p.Leu1764fs Pathogenic ★★★ same condition
- ATM p.Lys387fs Pathogenic ★★★ same condition
- ATM p.Lys468fs 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-phe657fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown