Is ATR p.Pro485= (c.1455T>C) pathogenic?

ATR p.Pro485= (c.1455T>C) is classified Likely benign in ATR (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-12). Very rare (popmax 0.00134%, afr); Associated with Inborn genetic diseases.

What condition is associated with ATR p.Pro485= (c.1455T>C)?

ATR p.Pro485= (c.1455T>C) is associated with Inborn genetic diseases (ClinVar).

How common is ATR p.Pro485= (c.1455T>C) in the general population?

ATR p.Pro485= (c.1455T>C) is very rare (popmax 0.00134%, afr) (gnomAD).

ATR p.Pro485=

c.1455T>C · rs1373293940 · VCV1773051

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

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 3.4	GERP 1.3, phastCons 1
Overall
CADD	9.3	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,906 alleles

Overall 6.2e-05% 1/1,613,648 alleles · very rare exomes 0/1,461,512 · genomes 1/152,136 · joint denominator

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: ATR
Protein: p.Pro485=
Coding: c.1455T>C
MANE Select: NM_001184
dbSNP: rs1373293940
Type: single nucleotide variant
Location: chr3:142560349 (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.Pro485Leu Uncertain significance ★ ⚠ same residue
ATR p.Pro485Ser 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

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-pro485 (accessed [today's date]).

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