Is ATR p.Ser1007= (c.3021C>T) pathogenic?

ATR p.Ser1007= (c.3021C>T) is classified Likely benign in ATR (ClinVar, Single submitter, 1 submitter; last evaluated 2020-03-13). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ATR p.Ser1007= (c.3021C>T)?

ATR p.Ser1007= (c.3021C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ATR p.Ser1007= (c.3021C>T) in the general population?

ATR p.Ser1007= (c.3021C>T) is absent from gnomAD v4.1 (gnomAD).

ATR p.Ser1007=

c.3021C>T · rs2108455043 · VCV1798922

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

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 2.2	GERP -0.79, phastCons 1
Overall
CADD	9.165	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: ATR
Protein: p.Ser1007=
Coding: c.3021C>T
MANE Select: NM_032208 · reported on NM_001184
dbSNP: rs2108455043
Type: single nucleotide variant
Location: chr3:142549629 (GRCh38)
Structure: AlphaFold pLDDT 72.76 · 5 PDB

Full ATR gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ATR p.Ser1007Asn Uncertain significance ★★ ⚠ same residue
ANTXR1 p.Ala26Val Uncertain significance ★★ ⚠ same condition
ANTXR1 p.Arg444Gln Uncertain significance ★★ ⚠ same condition
ANTXR1 p.Arg557Cys Uncertain significance ★★ ⚠ same condition
ANTXR1 p.Gly369Ser Uncertain significance ★★ ⚠ same condition
ANTXR1 p.Leu45Val Uncertain significance ★★ ⚠ same condition
ANTXR1 p.Pro524Leu Uncertain significance ★★ ⚠ same condition
ANTXR1 p.Pro534Gln Uncertain significance ★★ ⚠ 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/atr-p-ser1007 (accessed [today's date]).

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