C1QC p.Pro66=
c.198C>T · rs536551988 · VCV1599281
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.55%, 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 -6.3 | GERP -3.1 |
| Overall | ||
| CADD | 5.391 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.55%
South Asian · 501/91,084 alleles
Filtering AF
0.51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.494%
Overall
0.0339%
545/1,606,372 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.55% | 182 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,498 |
| East Asian | 0.00669% | 14,955 |
| African / African-American | 0.004% | 25,013 |
| Finnishnot grpmax-eligible | 0.00177% | 56,410 |
| European (non-Finnish) | 0.00102% | 98,327 |
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
- C1QC
- Protein
- p.Pro66=
- Coding
- c.198C>T
- MANE Select
- NM_172369
- dbSNP
- rs536551988
- Type
- single nucleotide variant
- Location
- chr1:22647243 (GRCh38)
- Gene constraint
- LOEUF 1.643 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 81.69 · 11 PDB
- Residue 66
- the collagen-like domain; the 'disordered' region
Similar variants
- C1QC p.Gly34Arg Pathogenic ★★ same type
- C1QC p.Ala172Val Uncertain significance ★★ ⚠ same type
- C1QC p.Arg126Gln Uncertain significance ★★ ⚠ same type
- C1QC p.Arg184His Uncertain significance ★★ ⚠ same type
- C1QC p.Asp2Asn Uncertain significance ★★ ⚠ same type
- C1QC p.Glu77Lys Uncertain significance ★★ ⚠ same type
- C1QC p.Gly67Arg Uncertain significance ★★ same type
- C1QC p.His171Gln 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/c1qc-p-pro66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown