STIL p.Pro960=
c.2880G>A · rs774354721 · VCV385719
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0395%, sas)
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 0.26 | GERP 0.055, phastCons 1 |
| Overall | ||
| CADD | 12.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0395%
South Asian · 36/91,078 alleles
Filtering AF
0.0293%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0258%
Overall
0.00316%
51/1,613,972 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0395% | 2,530 |
| Middle Eastern | 0.0329% | 3,042 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,415 |
| Finnishnot grpmax-eligible | 0.00469% | 21,335 |
| Admixed American | 0.00167% | 59,998 |
| European (non-Finnish) | 0.000254% | 393,342 |
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.Pro960=
- Coding
- c.2880G>A
- MANE Select
- NM_001048166
- dbSNP
- rs774354721
- Type
- single nucleotide variant
- Location
- chr1:47260489 (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 960
- the 'interaction with rbm14' region
Similar variants
- 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
- STIL p.Arg9Gln 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-pro960 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown