ARID2 p.Gly458=
c.1374C>T · rs201532081 · VCV745717
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
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 0.037 | GERP -4.2, phastCons 0.82 |
| Overall | ||
| CADD | 6.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/59,914 alleles
Filtering AF
0.00901%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00682%
Overall
0.00062%
10/1,613,664 alleles · ultra-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.Gly458=
- Coding
- c.1374C>T
- MANE Select
- NM_152641
- dbSNP
- rs201532081
- Type
- single nucleotide variant
- Location
- chr12:45839372 (GRCh38)
- Gene constraint
- LOEUF 0.224 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.30 · 2 PDB
- Residue 458
- 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-gly458 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown