SMARCA2 p.Pro579=
c.1737G>A · rs371544356 · VCV366206
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, eas)
Conditions
1
intellectual disability-sparse hair-brachydactyly syndrome
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 -1.6 | GERP -5.4 |
| Overall | ||
| CADD | 7.406 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,880 alleles
Filtering AF
0.0144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0137%
Overall
0.0138%
222/1,613,092 alleles · ultra-rare
exomes 209/1,460,770 · genomes 13/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,610 |
| European (non-Finnish) | 0.0164% | 6,110 |
| South Asian | 0.011% | 9,102 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,409 |
| African / African-American | 0.00667% | 15,003 |
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
- SMARCA2
- Protein
- p.Pro579=
- Coding
- c.1737G>A
- MANE Select
- NM_003070
- dbSNP
- rs371544356
- Type
- single nucleotide variant
- Location
- chr9:2070462 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 579
- the 'disordered' region
Similar variants
- SMARCA2 p.Pro579Leu Likely benign ★ same residue
- SMARCA2 p.Ala1160Gly Pathogenic ★★ same condition
- SMARCA2 p.Ala1201Val Pathogenic/Likely pathogenic ★★ same condition
- SMARCA2 p.Arg1105Cys Pathogenic ★★ same condition
- SMARCA2 p.Arg1105His Pathogenic ★★ same condition
- SMARCA2 p.Arg1105Pro Pathogenic/Likely pathogenic ★★ same condition
- SMARCA2 p.Arg1159Gln Pathogenic/Likely pathogenic ★★ same condition
- SMARCA2 p.Arg1159Gly Pathogenic ★★ 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/smarca2-p-pro579 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown