Is ATF2 p.Gln501= (c.1503G>A) pathogenic?

ATF2 p.Gln501= (c.1503G>A) is classified Likely benign in ATF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-20). Very rare (popmax 0.0099%, sas).

How common is ATF2 p.Gln501= (c.1503G>A) in the general population?

ATF2 p.Gln501= (c.1503G>A) is very rare (popmax 0.0099%, sas) (gnomAD).

ATF2 p.Gln501=

c.1503G>A · rs773341486 · VCV750476

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0099%, sas)

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 4.9	GERP 1.9, phastCons 1
Overall
CADD	10.73	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0099% South Asian · 9/90,934 alleles

Filtering AF 0.00514% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00376%

Overall 0.00143% 23/1,612,282 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0099%	10,104
Admixed American	0.00502%	19,906
African / African-American	0.00401%	24,952
Remaining individualsnot grpmax-eligible	0.00321%	31,174
European (non-Finnish)	0.000509%	196,543

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: ATF2
Protein: p.Gln501=
Coding: c.1503G>A
MANE Select: NM_000514 · reported on NM_001880
dbSNP: rs773341486
Type: single nucleotide variant
Location: chr2:175074624 (GRCh38)
Structure: AlphaFold pLDDT 75.29 · 4 PDB

Full ATF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GDNF c.*2213G>A Uncertain significance ★★ same type
GDNF c.*2828T>A Uncertain significance ★★ same type
GDNF p.Arg116Gln Uncertain significance ★★ ⚠ same type
ATF1 p.Tyr109= Benign ★★ same type
ATF2 p.Asn348= Benign ★★ same type
ATF2 p.Asp440= Benign ★★ same type
GDNF c.152-73C>T Benign ★★ same type
GDNF c.-51A>G Benign ★★ 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/atf2-p-gln501 (accessed [today's date]).

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