Is ATM p.Ser644= (c.1932A>T) pathogenic?

ATM p.Ser644= (c.1932A>T) is classified Conflicting classifications of pathogenicity in ATM (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2022-05-03). Absent from gnomAD v4.1; Associated with ataxia telangiectasia.

What condition is associated with ATM p.Ser644= (c.1932A>T)?

ATM p.Ser644= (c.1932A>T) is associated with ataxia telangiectasia, hereditary neoplastic syndrome (ClinVar).

How common is ATM p.Ser644= (c.1932A>T) in the general population?

ATM p.Ser644= (c.1932A>T) 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.

ATM p.Ser644=

c.1932A>T · rs1241804364 · VCV1782904

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

ataxia telangiectasia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.45	acceptor gain · deltas
Pangolin	Δ0.48	gain · loss 0.28 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 0.91	GERP -5.3, phastCons 0.98
Overall
CADD	16.86	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.Ser644=
Coding: c.1932A>T
MANE Select: NM_000051
dbSNP: rs1241804364
Type: single nucleotide variant
Location: chr11:108253847 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 644: 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

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

Also linked: hereditary neoplastic syndrome

For Ataxia-telangiectasia (Orphanet):

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

Similar variants

ATM p.Ser644Ter Pathogenic ★★ same residue
ATM p.Ser644Leu Uncertain significance ★ ⚠ same residue
ATM p.Ser644Pro Uncertain significance ★ ⚠ same residue
ATM p.Ser644Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
ATM p.Ser644delinsArgTer Pathogenic/Likely pathogenic ★★ same residue
ATM p.Ser644fs 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-ser644 (accessed [today's date]).

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