SMARCD2 p.Pro114=
c.342A>G · rs1162508392 · VCV1392982
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.2 | GERP -3.7, phastCons 0.99 |
| Overall | ||
| CADD | 12.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/6,004 alleles
Filtering AF
0.00556%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00398%
Overall
0.000813%
13/1,598,242 alleles · ultra-rare
exomes 10/1,446,070 · genomes 3/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 6,004 |
| Admixed American | 0.012% | 8,360 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,843 |
| European (non-Finnish) | 0.000256% | 390,093 |
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.Pro114=
- Coding
- c.342A>G
- MANE Select
- NM_001098426
- dbSNP
- rs1162508392
- Type
- single nucleotide variant
- Location
- chr17:63837500 (GRCh38)
- Gene constraint
- LOEUF 0.762 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38
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-pro114 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown