Is ARID2 p.Ser1550Arg (c.4650C>G) pathogenic?

ARID2 p.Ser1550Arg (c.4650C>G) is classified Uncertain significance in ARID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-29). AlphaMissense: likely pathogenic (0.8883); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ARID2 p.Ser1550Arg (c.4650C>G)?

ARID2 p.Ser1550Arg (c.4650C>G) is associated with Inborn genetic diseases (ClinVar).

How common is ARID2 p.Ser1550Arg (c.4650C>G) in the general population?

ARID2 p.Ser1550Arg (c.4650C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARID2 p.Ser1550Arg (c.4650C>G)?

AlphaMissense predicts likely pathogenic (score 0.8883) — an in-silico prediction, not a clinical call.

ARID2 p.Ser1550Arg

c.4650C>G · VCV3945834

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8883 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8883	likely pathogenic
REVEL	0.336	indeterminate
SaProt	LLR -8.12	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 0.11	GERP -2.3, phastCons 0.98
Regional constraint	o/e 0.72	unconstrained · MANE · 39 kb · p 0.00053 · regional, not allelic
Overall
CADD	20.7	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ARID2
Protein: p.Ser1550Arg
Coding: c.4650C>G
MANE Select: NM_152641
Type: single nucleotide variant
Location: chr12:45852773 (GRCh38)
Gene constraint: LOEUF 0.224 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 52.30 · 2 PDB
Residue 1550: a UniProt-annotated variant site (in css6)

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-ser1550arg (accessed [today's date]).

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