ARID2 p.Ser1229=
c.3687A>G · VCV3770813
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0245%, eas)
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 -1.2 | GERP -5.2 |
| Overall | ||
| CADD | 1.432 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0245%
East Asian · 11/44,872 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00235%
38/1,614,124 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0245% | 4,079 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.00329% | 30,361 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,253 |
| European (non-Finnish) | 0.00169% | 59,000 |
| Admixed American | 0.00167% | 60,008 |
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.Ser1229=
- Coding
- c.3687A>G
- MANE Select
- NM_152641
- Type
- single nucleotide variant
- Location
- chr12:45851810 (GRCh38)
- Gene constraint
- LOEUF 0.224 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.30 · 2 PDB
- Residue 1229
- a UniProt-annotated variant site (in css6)
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-ser1229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown