Is ATM p.Ser974= (c.2922C>T) pathogenic?

ATM p.Ser974= (c.2922C>T) is classified Conflicting classifications of pathogenicity in ATM (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-26). Very rare (popmax 0.000339%, nfe); Associated with ataxia telangiectasia.

What condition is associated with ATM p.Ser974= (c.2922C>T)?

ATM p.Ser974= (c.2922C>T) is associated with ataxia telangiectasia, hereditary breast ovarian cancer syndrome, hereditary neoplastic syndrome (ClinVar).

How common is ATM p.Ser974= (c.2922C>T) in the general population?

ATM p.Ser974= (c.2922C>T) is very rare (popmax 0.000339%, nfe) (gnomAD).

How is Ataxia-telangiectasia inherited?

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

ATM p.Ser974=

c.2922C>T · rs758045139 · VCV229690

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Conditions

ataxia telangiectasia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.11	GERP 0.32, phastCons 0.22
Overall
CADD	12.96	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,179,272 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000274% 4/1,461,082 alleles · very rare

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.Ser974=
Coding: c.2922C>T
MANE Select: NM_000051
dbSNP: rs758045139
Type: single nucleotide variant
Location: chr11:108271251 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 974: 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

Also linked: hereditary breast ovarian cancer syndrome hereditary neoplastic syndrome

For Ataxia-telangiectasia (Orphanet):

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

Similar variants

ATM p.Ser974Cys Uncertain significance ★★ ⚠ same residue
ATM p.Ser974Phe Uncertain significance ★★ same residue
ATM p.Ser974Pro Uncertain significance ★★ ⚠ same residue
ATM p.Ser974Tyr 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

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-ser974 (accessed [today's date]).

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