Is ATM p.Lys892Thr (c.2675A>C) pathogenic?

ATM p.Lys892Thr (c.2675A>C) is classified Uncertain significance in ATM (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-06). AlphaMissense: likely benign (0.2167); Absent from gnomAD v4.1; Associated with ataxia telangiectasia.

What condition is associated with ATM p.Lys892Thr (c.2675A>C)?

ATM p.Lys892Thr (c.2675A>C) is associated with ataxia telangiectasia (ClinVar).

How common is ATM p.Lys892Thr (c.2675A>C) in the general population?

ATM p.Lys892Thr (c.2675A>C) is absent from gnomAD v4.1 (gnomAD).

How is Ataxia-telangiectasia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about ATM p.Lys892Thr (c.2675A>C)?

AlphaMissense predicts likely benign (score 0.2167) — an in-silico prediction, not a clinical call.

ATM p.Lys892Thr

c.2675A>C · rs1476268748 · VCV2812461

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2167 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

ataxia telangiectasia

Computational evidence

Protein change
AlphaMissense	0.2167	likely benign
REVEL	0.338	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>G here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.9	GERP 1.5, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 66 kb · p 0.75 · regional, not allelic
Overall
CADD	22.0	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.Lys892Thr
Coding: c.2675A>C
MANE Select: NM_000051
dbSNP: rs1476268748
Type: single nucleotide variant
Location: chr11:108268446 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 892: 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

ataxia telangiectasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Ataxia-telangiectasia (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy
Prevalence: 1-5 / 10 000 (Norway)

Similar variants

ATM p.Lys892Asn Uncertain significance ★★ same residue
ATM p.Lys892Glu Uncertain significance ★★ ⚠ same residue
ATM p.Lys892Ter Likely pathogenic ★ same residue
ATM p.Lys892= Likely benign ★ 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

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-lys892thr (accessed [today's date]).

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