Is ARID1A p.Pro697= (c.2091G>A) pathogenic?

ARID1A p.Pro697= (c.2091G>A) is classified Likely benign in ARID1A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-04-24). Ultra-rare (popmax 0.01%, amr); Associated with Inborn genetic diseases.

What condition is associated with ARID1A p.Pro697= (c.2091G>A)?

ARID1A p.Pro697= (c.2091G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ARID1A p.Pro697= (c.2091G>A) in the general population?

ARID1A p.Pro697= (c.2091G>A) is ultra-rare (popmax 0.01%, amr) (gnomAD).

ARID1A p.Pro697=

c.2091G>A · rs990716737 · VCV1325947

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.01%, amr)

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 -11	GERP -4.7
Overall
CADD	0.246	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.01% Admixed American · 6/59,980 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.00279% 45/1,613,748 alleles · ultra-rare exomes 40/1,461,840 · genomes 5/151,908 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.01%	9,997
Remaining individualsnot grpmax-eligible	0.0064%	15,622
East Asian	0.00446%	22,437
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,598
European (non-Finnish)	0.00263%	38,064
African / African-American	0.00134%	74,808

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: ARID1A
Protein: p.Pro697=
Coding: c.2091G>A
MANE Select: NM_006015
dbSNP: rs990716737
Type: single nucleotide variant
Location: chr1:26761026 (GRCh38)
Gene constraint: LOEUF 0.141 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 47.81 · 7 PDB
Residue 697: the 'disordered' region

Full ARID1A 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

ARID1A p.Ala1489Val Uncertain significance ★★ ⚠ same condition
ARID1A p.Ala196Val Uncertain significance ★★ ⚠ same condition
ARID1A p.Ala2099Ser Uncertain significance ★★ ⚠ same condition
ARID1A p.Ala325Gly Uncertain significance ★★ ⚠ same condition
ARID1A p.Ala330Val Uncertain significance ★★ ⚠ same condition
ARID1A p.Arg1109Trp Uncertain significance ★★ ⚠ same condition
ARID1A p.Arg1980His Uncertain significance ★★ ⚠ same condition
ARID1A p.Arg2183His 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/arid1a-p-pro697 (accessed [today's date]).

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