SMARCD2 p.Leu313=
c.937T>C · rs768534738 · VCV1540985
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, amr)
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 -0.43 | GERP -4.8, phastCons 0.001 |
| Overall | ||
| CADD | 1.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
Admixed American · 8/59,790 alleles
Filtering AF
0.00664%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00484%
Overall
0.0013%
21/1,612,366 alleles · ultra-rare
exomes 17/1,460,212 · genomes 4/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0134% | 7,474 |
| African / African-American | 0.00134% | 74,868 |
| European (non-Finnish) | 0.00102% | 98,254 |
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
- SMARCD2
- Protein
- p.Leu313=
- Coding
- c.937T>C
- MANE Select
- NM_001098426
- dbSNP
- rs768534738
- Type
- single nucleotide variant
- Location
- chr17:63834313 (GRCh38)
- Gene constraint
- LOEUF 0.762 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38
- Residue 313
- the swib/mdm2 domain
Similar variants
- SMARCD2 p.Arg192Ter Pathogenic/Likely pathogenic ★★ same type
- SMARCD2 c.922-3C>T Uncertain significance ★★ same type
- SMARCD2 p.Ala434Thr Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Ala6Val Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Arg118Cys Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Arg148Gln Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Arg150Trp Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Arg175His 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/smarcd2-p-leu313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown