SMARCA4 p.Pro683=
c.2049C>G · VCV4085788
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.8 |
| Overall | ||
| CADD | 0.288 | PHRED · no single calibrated threshold — expert panels disagree |
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
- SMARCA4
- Protein
- p.Pro683=
- Coding
- c.2049C>G
- MANE Select
- NM_003072
- Type
- single nucleotide variant
- Location
- chr19:11007949 (GRCh38)
- Gene constraint
- LOEUF 0.226 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.38 · 31 PDB
- Residue 683
- the 'disordered' region; the 'rna-binding region which is sufficient for binding to lncrna evf2' region
Similar variants
- SMARCA4 p.Pro683Leu Uncertain significance ★★ ⚠ same residue
- SMARCA4 p.Pro683Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
- SMARCA4 c.1943+1G>A Likely pathogenic ★★ same type
- SMARCA4 c.2274+1G>T Likely pathogenic ★★ same type
- SMARCA4 c.2438+1G>A Pathogenic/Likely pathogenic ★★ same type
- SMARCA4 c.3216-1G>C Likely pathogenic ★★ same type
- SMARCA4 c.3216-2A>G Likely pathogenic ★★ same type
- SMARCA4 c.3546+1G>A Likely 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/smarca4-p-pro683 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown