ATM p.Ser83Pro
c.247T>C · VCV3383761
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.4694 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4694 | ambiguous |
|---|---|---|
| REVEL | 0.192 | benign-leaning |
| SaProt | — | not scored · why |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 2.7, phastCons 1 |
| Regional constraint | o/e 0.99 | unconstrained · MANE · 66 kb · p 0.75 · regional, not allelic |
| Overall | ||
| CADD | 24.4 | 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
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.Ser83Pro
- Coding
- c.247T>C
- MANE Select
- NM_000051
- Type
- single nucleotide variant
- Location
- chr11:108229239 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Residue 83
- a UniProt-annotated variant site (in at)
Similar variants
- ATM p.Ser83Ter Pathogenic ★★ same residue
- ATM p.Ser83Leu Uncertain significance ★★ ⚠ same residue
- ATM p.Ser83= Likely benign ★★ same residue
- ATM p.Ser83fs Pathogenic ★ same residue
- ATM c.1607+1G>T Pathogenic ★★★ same type
- ATM c.2251-2A>T Pathogenic ★★★ same type
- ATM c.2251-4A>G Likely pathogenic ★★★ same type
- ATM c.2466+5G>C Likely pathogenic ★★★ same type
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-ser83pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown