RUSC2 p.Pro953=
c.2859G>A · rs878072 · VCV1599160
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.772%, afr)
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 -4 | GERP -3.9 |
| Overall | ||
| CADD | 1.213 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.772%
African / African-American · 579/75,026 alleles
Filtering AF
0.72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.699%
Overall
0.104%
1,680/1,614,146 alleles · rare
exomes 1,296/1,461,828 · genomes 384/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.772% | 130 |
| South Asian | 0.176% | 569 |
| Remaining individualsnot grpmax-eligible | 0.072% | 1,389 |
| European (non-Finnish) | 0.07% | 1,429 |
| Admixed American | 0.07% | 1,429 |
| Middle Eastern | 0.0495% | 2,021 |
| Finnishnot grpmax-eligible | 0.0359% | 2,784 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,800 |
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.Pro953=
- Coding
- c.2859G>A
- MANE Select
- NM_014806
- dbSNP
- rs878072
- Type
- single nucleotide variant
- Location
- chr9:35556324 (GRCh38)
- Gene constraint
- LOEUF 0.383 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 45.82 · 1 PDB
- Residue 953
- 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-pro953 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown