SMARCE1 p.Arg201=
c.603C>T · VCV4935074
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.11 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.4 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 14.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Overall
6.84e-05%
1/1,461,708 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
- SMARCE1
- Protein
- p.Arg201=
- Coding
- c.603C>T
- MANE Select
- NM_003079
- Type
- single nucleotide variant
- Location
- chr17:40632306 (GRCh38)
- Gene constraint
- LOEUF 0.318 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 70.72 · 8 PDB
- Residue 201
- an α-helix
Similar variants
- SMARCE1 p.Arg201Cys Uncertain significance ★★ ⚠ same residue
- SMARCE1 p.Arg201His Uncertain significance ★★ same residue
- SMARCE1 p.Arg201fs Pathogenic ★ same residue
- SMARCE1 c.237+1G>T Pathogenic ★★ same type
- SMARCE1 p.Arg105Gln Pathogenic/Likely pathogenic ★★ same type
- SMARCE1 p.Arg158Ter Pathogenic ★★ same type
- SMARCE1 p.Arg239Ter Pathogenic ★★ same type
- SMARCE1 p.Arg251Ter Pathogenic/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/smarce1-p-arg201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown