Is ARID2 p.Arg314His (c.941G>A) pathogenic?

ARID2 p.Arg314His (c.941G>A) is classified Uncertain significance in ARID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-16). AlphaMissense: likely pathogenic (0.9438); Very rare (popmax 8.47e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ARID2 p.Arg314His (c.941G>A)?

ARID2 p.Arg314His (c.941G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ARID2 p.Arg314His (c.941G>A) in the general population?

ARID2 p.Arg314His (c.941G>A) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

What do computational predictors say about ARID2 p.Arg314His (c.941G>A)?

AlphaMissense predicts likely pathogenic (score 0.9438) — an in-silico prediction, not a clinical call.

ARID2 p.Arg314His

c.941G>A · rs916056847 · VCV2292588

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9438 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9438	likely pathogenic
REVEL	0.643	indeterminate
SaProt	LLR -6.42	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.4, phastCons 1
Regional constraint	o/e 0.43	unconstrained · MANE · 2,528 bp · p 5.5e-16 · regional, not allelic
Overall
CADD	34.0	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 8.47e-05% European (non-Finnish) · 1/1,179,978 alleles

Overall 6.84e-05% 1/1,461,802 alleles · very rare

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.Arg314His
Coding: c.941G>A
MANE Select: NM_152641
dbSNP: rs916056847
Type: single nucleotide variant
Location: chr12:45836909 (GRCh38)
Gene constraint: LOEUF 0.224 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 52.30 · 2 PDB
Residue 314: an α-helix

Full ARID2 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

ARID2 p.Arg1769Ter Pathogenic ★★ same condition
ARID2 p.Ala1335Glu Uncertain significance ★★ ⚠ same condition
ARID2 p.Asn1280Asp Uncertain significance ★★ ⚠ same condition
ARID2 p.Asp1400Gly Uncertain significance ★★ ⚠ same condition
ARID2 p.Gln752Lys Uncertain significance ★★ ⚠ same condition
ARID2 p.Ile943Phe Uncertain significance ★★ ⚠ same condition
ARID2 p.Ser990Leu Uncertain significance ★★ ⚠ same condition
ARID2 p.Thr1474Ala 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/arid2-p-arg314his (accessed [today's date]).

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