Is ATF3 p.Ser28= (c.84A>C) pathogenic?

ATF3 p.Ser28= (c.84A>C) is classified Likely benign in ATF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-20). Absent from gnomAD v4.1.

How common is ATF3 p.Ser28= (c.84A>C) in the general population?

ATF3 p.Ser28= (c.84A>C) is absent from gnomAD v4.1 (gnomAD).

ATF3 p.Ser28=

c.84A>C · VCV4643738

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 1.2	GERP -1.3, phastCons 1
Overall
CADD	9.971	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: ATF3
Protein: p.Ser28=
Coding: c.84A>C
MANE Select: NM_001674
Type: single nucleotide variant
Location: chr1:212615105 (GRCh38)
Gene constraint: LOEUF 0.879 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 77.45

Full ATF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ATF3 p.Ser12Pro Uncertain significance ★★ ⚠ same type
ATF3 p.Ala82Val Uncertain significance ★ ⚠ same type
ATF3 p.Asn168Ile Uncertain significance ★ ⚠ same type
ATF3 p.Asp69Asn Uncertain significance ★ ⚠ same type
ATF3 p.Gln115Glu Uncertain significance ★ ⚠ same type
ATF3 p.Glu32Lys Uncertain significance ★ ⚠ same type
ATF3 p.Glu80Lys Uncertain significance ★ ⚠ same type
ATF3 p.Ile171Thr Uncertain significance ★ ⚠ same type

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/atf3-p-ser28 (accessed [today's date]).

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