Is ATM p.Ser2209= (c.6627C>G) pathogenic?

ATM p.Ser2209= (c.6627C>G) is classified Likely benign in ATM (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-06-26). Absent from gnomAD v4.1; Associated with ataxia telangiectasia.

What condition is associated with ATM p.Ser2209= (c.6627C>G)?

ATM p.Ser2209= (c.6627C>G) is associated with ataxia telangiectasia, hereditary neoplastic syndrome (ClinVar).

How common is ATM p.Ser2209= (c.6627C>G) in the general population?

ATM p.Ser2209= (c.6627C>G) 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.Ser2209=

c.6627C>G · rs2085556098 · VCV922864

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple 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 carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.3	GERP -0.85
Overall
CADD	7.576	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.Ser2209=
Coding: c.6627C>G
MANE Select: NM_152587 · reported on NM_000051
dbSNP: rs2085556098
Type: single nucleotide variant
Location: chr11:108325364 (GRCh38)

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)

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-ser2209 (accessed [today's date]).

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