Is ATR p.Ser79Phe (c.236C>T) pathogenic?

ATR p.Ser79Phe (c.236C>T) is classified Uncertain significance in ATR (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-15). AlphaMissense: ambiguous (0.3531); Very rare (popmax 0.0011%, sas); Associated with Inborn genetic diseases.

What condition is associated with ATR p.Ser79Phe (c.236C>T)?

ATR p.Ser79Phe (c.236C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ATR p.Ser79Phe (c.236C>T) in the general population?

ATR p.Ser79Phe (c.236C>T) is very rare (popmax 0.0011%, sas) (gnomAD).

What do computational predictors say about ATR p.Ser79Phe (c.236C>T)?

AlphaMissense predicts ambiguous (score 0.3531) — an in-silico prediction, not a clinical call.

ATR p.Ser79Phe

c.236C>T · rs2108494163 · VCV2567832

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3531 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3531	ambiguous
REVEL	0.079	moderately benign-leaning
SaProt	LLR -4.26	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.8	GERP 2.1, phastCons 1
Overall
CADD	22.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,076 alleles

Overall 6.84e-05% 1/1,461,848 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: ATR
Protein: p.Ser79Phe
Coding: c.236C>T
MANE Select: NM_032208 · reported on NM_001184
dbSNP: rs2108494163
Type: single nucleotide variant
Location: chr3:142566177 (GRCh38)
Structure: AlphaFold pLDDT 72.76 · 5 PDB
Residue 79: a disulfide bond; a β-strand; the vwfa domain

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.Ser79= Likely benign ★★ 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-ser79phe (accessed [today's date]).

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