C1QBP p.Pro9=
c.27C>T · rs1312010462 · VCV1551259
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00263%, nfe)
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 2.1 | phastCons 1 |
| Overall | ||
| CADD | 8.939 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00263%
European (non-Finnish) · 30/1,139,162 alleles
Filtering AF
0.00187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.00222%
34/1,530,274 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00263% | 37,972 |
| East Asian | 0.00262% | 38,108 |
| South Asian | 0.0024% | 41,699 |
| Remaining individualsnot grpmax-eligible | 0.00169% | 59,100 |
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
- C1QBP
- Protein
- p.Pro9=
- Coding
- c.27C>T
- MANE Select
- NM_001212
- dbSNP
- rs1312010462
- Type
- single nucleotide variant
- Location
- chr17:5439047 (GRCh38)
- Gene constraint
- LOEUF 1.155 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.12 · 4 PDB
Similar variants
- C1QBP p.Pro9Arg Uncertain significance ★ ⚠ same residue
- C1QBP p.Phe204Leu Pathogenic/Likely pathogenic ★★ same type
- C1QBP p.Ala81Gly Uncertain significance ★★ ⚠ same type
- C1QBP p.Asn134Ser Uncertain significance ★★ ⚠ same type
- C1QBP p.Glu196Asp Uncertain significance ★★ ⚠ same type
- C1QBP p.Glu93Asp Uncertain significance ★★ ⚠ same type
- C1QBP p.Lys179Thr Uncertain significance ★★ ⚠ same type
- C1QBP p.Pro149Ser 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/c1qbp-p-pro9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown