SMARCD2 p.Thr201=
c.603G>A · VCV4936554
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, 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 -14 | GERP -4.8 |
| Overall | ||
| CADD | 2.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,004 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.00112%
18/1,613,856 alleles · very rare
exomes 14/1,461,658 · genomes 4/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,002 |
| South Asian | 0.0022% | 45,545 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
| Finnishnot grpmax-eligible | 0.00156% | 64,008 |
| African / African-American | 0.00133% | 74,908 |
| European (non-Finnish) | 0.000932% | 107,262 |
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.Thr201=
- Coding
- c.603G>A
- MANE Select
- NM_001098426
- Type
- single nucleotide variant
- Location
- chr17:63835532 (GRCh38)
- Gene constraint
- LOEUF 0.762 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38
Similar variants
- SMARCD2 p.Thr201Met Benign ★ ⚠ same residue
- 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
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-thr201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown