Is ARID2 p.Ala810Pro (c.2428G>C) pathogenic?

ARID2 p.Ala810Pro (c.2428G>C) is classified Benign/Likely benign in ARID2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-06-01). AlphaMissense: likely benign (0.1003); Low-frequency (popmax 1.38%, eas).

How common is ARID2 p.Ala810Pro (c.2428G>C) in the general population?

ARID2 p.Ala810Pro (c.2428G>C) is low-frequency (popmax 1.38%, eas) (gnomAD).

What do computational predictors say about ARID2 p.Ala810Pro (c.2428G>C)?

AlphaMissense predicts likely benign (score 0.1003) — an in-silico prediction, not a clinical call.

ARID2 p.Ala810Pro

c.2428G>C · rs74916892 · VCV133566

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.1003 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.38%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1003	likely benign
REVEL	0.031	moderately benign-leaning
SaProt	LLR -6.59	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.1	GERP 0.094, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 12 kb · p 0.0001 · regional, not allelic
Overall
CADD	16.67	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 1.38% East Asian · 619/44,872 alleles

Filtering AF 1.29% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.25%

Overall 0.0454% 733/1,614,096 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	1.38%	72
Remaining individualsnot grpmax-eligible	0.142%	702
African / African-American	0.0227%	4,414
South Asian	0.0022%	45,543
Admixed American	0.00167%	60,006
European (non-Finnish)	0.000424%	236,000

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: ARID2
Protein: p.Ala810Pro
Coding: c.2428G>C
MANE Select: NM_152641
dbSNP: rs74916892
Type: single nucleotide variant
Location: chr12:45850551 (GRCh38)
Gene constraint: LOEUF 0.224 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 52.30 · 2 PDB
Residue 810: a UniProt-annotated variant site (in css6)

Full ARID2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARID2 p.Arg1272Ter Pathogenic ★★ same type
ARID2 p.Arg1677Ter Pathogenic/Likely pathogenic ★★ same type
ARID2 p.Arg1754Ter Pathogenic ★★ same type
ARID2 p.Arg1769Ter Pathogenic ★★ same type
ARID2 p.Arg274Ter Pathogenic/Likely pathogenic ★★ same type
ARID2 p.Gln920Ter Pathogenic ★★ same type
ARID2 p.Ala1335Glu Uncertain significance ★★ ⚠ same type
ARID2 p.Arg1679Gln 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/arid2-p-ala810pro (accessed [today's date]).

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