RUSC2 p.Pro1329=
c.3987T>A · rs547335067 · VCV1953848
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00511%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -3.2, phastCons 0.002 |
| Overall | ||
| CADD | 5.248 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00511%
Admixed American · 3/58,760 alleles
Filtering AF
0.00136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000676%
Overall
0.000187%
3/1,607,580 alleles · very rare
exomes 1/1,455,330 · genomes 2/152,250 · joint denominator
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
- RUSC2
- Protein
- p.Pro1329=
- Coding
- c.3987T>A
- MANE Select
- NM_014806
- dbSNP
- rs547335067
- Type
- single nucleotide variant
- Location
- chr9:35560627 (GRCh38)
- Gene constraint
- LOEUF 0.383 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 45.82 · 1 PDB
- Residue 1329
- the 'disordered' region; a UniProt-annotated variant site (in mrt61; uncertain significance)
Similar variants
- RUSC2 p.Arg1393Ter Pathogenic/Likely pathogenic ★★ same type
- RUSC2 p.Ala1054Thr Uncertain significance ★★ ⚠ same type
- RUSC2 p.Ala1268Thr Uncertain significance ★★ ⚠ same type
- RUSC2 p.Ala126Thr Uncertain significance ★★ ⚠ same type
- RUSC2 p.Ala319Thr Uncertain significance ★★ ⚠ same type
- RUSC2 p.Ala585Thr Uncertain significance ★★ ⚠ same type
- RUSC2 p.Ala745Thr Uncertain significance ★★ ⚠ same type
- RUSC2 p.Ala886Asp 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/rusc2-p-pro1329 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown