STIL p.Ser409=
c.1227T>C · rs200532713 · VCV193861
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, 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 6.8 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 12.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/60,012 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0101%
Overall
0.00329%
53/1,611,856 alleles · ultra-rare
exomes 47/1,459,554 · genomes 6/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,616 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,818 |
| European (non-Finnish) | 0.00305% | 32,743 |
| African / African-American | 0.00133% | 75,016 |
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
- STIL
- Protein
- p.Ser409=
- Coding
- c.1227T>C
- MANE Select
- NM_001048166
- dbSNP
- rs200532713
- Type
- single nucleotide variant
- Location
- chr1:47282366 (GRCh38)
- Gene constraint
- LOEUF 0.575 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 54.29 · 5 PDB
- Residue 409
- the 'interaction with rbm14' region; the 'interaction with cpap' region; the 'disordered' region
Similar variants
- STIL p.Ser409Thr Likely pathogenic ★ ⚠ same residue
- STIL c.*203C>T Uncertain significance ★★ same type
- STIL c.*599A>G Uncertain significance ★★ same type
- STIL p.Ala213Val Uncertain significance ★★ ⚠ same type
- STIL p.Ala543Val Uncertain significance ★★ ⚠ same type
- STIL p.Arg1004Gly Uncertain significance ★★ ⚠ same type
- STIL p.Arg67Cys Uncertain significance ★★ ⚠ same type
- STIL p.Arg742His 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/stil-p-ser409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown