C1QB p.Pro163=
c.489C>T · rs140417615 · VCV753564
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.229%, 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 -20 | GERP -3.9 |
| Overall | ||
| CADD | 3.938 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.229%
African / African-American · 172/75,022 alleles
Filtering AF
0.201%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.191%
Overall
0.0125%
201/1,614,154 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.229% | 436 |
| Admixed American | 0.0183% | 5,457 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,419 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
| European (non-Finnish) | 0.000932% | 107,274 |
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
- C1QB
- Protein
- p.Pro163=
- Coding
- c.489C>T
- MANE Select
- NM_001378156
- dbSNP
- rs140417615
- Type
- single nucleotide variant
- Location
- chr1:22661119 (GRCh38)
- Gene constraint
- LOEUF 1.001 · pLI 0.25 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 79.87 · 11 PDB
- Residue 163
- the c1q domain
Similar variants
- C1QB p.Pro163His Uncertain significance ★ ⚠ same residue
- C1QB p.Pro163Leu Uncertain significance ★ ⚠ same residue
- C1QB p.Arg175Ter Likely pathogenic ★★ same type
- C1QB p.Ala121Thr Uncertain significance ★★ ⚠ same type
- C1QB p.Ala124Asp Uncertain significance ★★ ⚠ same type
- C1QB p.Arg134Gln Uncertain significance ★★ ⚠ same type
- C1QB p.Arg134Trp Uncertain significance ★★ ⚠ same type
- C1QB p.Arg186Gln 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/c1qb-p-pro163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown