ARID1A p.Pro408=
c.1224G>A · rs139540163 · VCV2638530
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0419%, nfe)
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 -2.6 | GERP -4.7 |
| Overall | ||
| CADD | 8.454 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0419%
European (non-Finnish) · 495/1,180,024 alleles
Filtering AF
0.0389%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0377%
Overall
0.0327%
528/1,614,208 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0419% | 2,384 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,677 |
| East Asian | 0.00891% | 11,223 |
| Finnishnot grpmax-eligible | 0.00625% | 16,009 |
| African / African-American | 0.00533% | 18,762 |
| Admixed American | 0.005% | 20,010 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- ARID1A
- Protein
- p.Pro408=
- Coding
- c.1224G>A
- MANE Select
- NM_006015
- dbSNP
- rs139540163
- Type
- single nucleotide variant
- Location
- chr1:26729737 (GRCh38)
- Gene constraint
- LOEUF 0.141 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 47.81 · 7 PDB
- Residue 408
- the 'disordered' region
Similar variants
- ARID1A p.Pro408Leu Likely benign ★ same residue
- ARID1A c.1920+5G>A Likely pathogenic ★★ same type
- ARID1A c.3198+5G>A Likely pathogenic ★★ same type
- ARID1A p.Ala1077Glu Pathogenic/Likely pathogenic ★★ same type
- ARID1A p.Arg1020Lys Likely pathogenic ★★ same type
- ARID1A p.Gln1367= Likely pathogenic ★★ same type
- ARID1A p.Gln199Ter Likely pathogenic ★★ same type
- ARID1A p.Gln450Ter Pathogenic ★★ 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/arid1a-p-pro408 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown