Is ARID2 p.Ala290fs (c.869_881del) pathogenic?

ARID2 p.Ala290fs (c.869881del) is classified Pathogenic in ARID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-18). Absent from gnomAD; Associated with Coffin-Siris syndrome 6.

What condition is associated with ARID2 p.Ala290fs (c.869_881del)?

ARID2 p.Ala290fs (c.869_881del) is associated with Coffin-Siris syndrome 6 (ClinVar).

How common is ARID2 p.Ala290fs (c.869_881del) in the general population?

ARID2 p.Ala290fs (c.869_881del) is absent from gnomAD (gnomAD).

ARID2 p.Ala290fs

c.869_881del · rs2547651122 · VCV2691005

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Coffin-Siris syndrome 6

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 8 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.92	GERP -4.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ARID2
Protein: p.Ala290fs
Coding: c.869_881del
MANE Select: NM_152641
dbSNP: rs2547651122
Type: Deletion
Location: chr12:45836836 (GRCh38)
Gene constraint: LOEUF 0.224 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 52.30 · 2 PDB
Residue 290: an α-helix

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

Disease context

Coffin-Siris syndrome 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ARID2 p.Ala1547fs Pathogenic ★ same condition
ARID2 p.Ala956fs Likely pathogenic ★ same condition
ARID2 p.Gln995fs Likely pathogenic ★ same condition
ARID2 p.Gly1139fs Pathogenic ★ same condition
ARID2 p.Gly1310fs Likely pathogenic ★ same condition
ARID2 p.His595fs Pathogenic ★ same condition
ARID2 p.Ile1376fs Likely pathogenic ★ same condition
ARID2 p.Leu330_Gly336del Likely pathogenic ★ 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/arid2-p-ala290fs (accessed [today's date]).

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