SMARCD1 p.Pro275=
c.825G>C · rs1050726 · VCV1711340
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, 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 -0.48 | GERP -1.6 |
| Overall | ||
| CADD | 4.512 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,180,018 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.00031%
5/1,614,030 alleles · very rare
exomes 4/1,461,854 · genomes 1/152,176 · joint denominator
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
- SMARCD1
- Protein
- p.Pro275=
- Coding
- c.825G>C
- MANE Select
- NM_003076
- dbSNP
- rs1050726
- Type
- single nucleotide variant
- Location
- chr12:50089937 (GRCh38)
- Gene constraint
- LOEUF 0.339 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.37 · 12 PDB
- Residue 275
- the 'interaction with smarcc1 and smarcc2' region; the 'necessary for gr/nr3c1-mediated remodeling and transcription from chromatin; required for gr/nr3c1 interaction with the brg1/smarca4 complex in vivo' region
Similar variants
- SMARCD1 p.Pro275Ser Uncertain significance ★ ⚠ same residue
- SMARCD1 p.Ala302Gly Uncertain significance ★★ same type
- SMARCD1 p.Arg334Gln Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Asp247Gly Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Ile184Val Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Ile323Val Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Thr189Ser Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Thr203Met 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/smarcd1-p-pro275 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown