Is ATF3 p.Ser24= (c.72C>T) pathogenic?

ATF3 p.Ser24= (c.72C>T) is classified Likely benign in ATF3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-28). Rare (popmax 0.245%, afr); Associated with ATF3-related disorder.

What condition is associated with ATF3 p.Ser24= (c.72C>T)?

ATF3 p.Ser24= (c.72C>T) is associated with ATF3-related disorder (ClinVar).

How common is ATF3 p.Ser24= (c.72C>T) in the general population?

ATF3 p.Ser24= (c.72C>T) is rare (popmax 0.245%, afr) (gnomAD).

ATF3 p.Ser24=

c.72C>T · rs148364357 · VCV3041761

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.245%, afr)

Conditions

ATF3-related disorder

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 0.31	GERP -1, phastCons 0.98
Overall
CADD	8.634	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.245% African / African-American · 184/75,018 alleles

Filtering AF 0.216% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.205%

Overall 0.0127% 205/1,614,158 alleles · rare exomes 84/1,461,892 · genomes 121/152,266 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.245%	408
Remaining individualsnot grpmax-eligible	0.0224%	4,465
Admixed American	0.01%	10,002
South Asian	0.0011%	91,084

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: ATF3
Protein: p.Ser24=
Coding: c.72C>T
MANE Select: NM_001674
dbSNP: rs148364357
Type: single nucleotide variant
Location: chr1:212615093 (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

Disease context

ATF3-related disorder

Similar variants

ATF3 p.Ser24Cys Uncertain significance ★ ⚠ same residue
ATF3 p.Ser24Phe Uncertain significance ★ same residue
ATF3 c.*6C>T Benign same condition
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

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-ser24 (accessed [today's date]).

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