C1QC p.Ala172=
c.516G>A · rs369658525 · VCV1541132
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.035%, amr)
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 -8.9 | GERP -3.1 |
| Overall | ||
| CADD | 2.683 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.035%
Admixed American · 21/60,032 alleles
Filtering AF
0.0234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.0139%
225/1,614,204 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.035% | 2,859 |
| European (non-Finnish) | 0.0165% | 6,051 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| South Asian | 0.0022% | 45,541 |
| African / African-American | 0.00133% | 75,042 |
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.Ala172=
- Coding
- c.516G>A
- MANE Select
- NM_172369
- dbSNP
- rs369658525
- Type
- single nucleotide variant
- Location
- chr1:22647561 (GRCh38)
- Gene constraint
- LOEUF 1.643 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 81.69 · 11 PDB
- Residue 172
- the c1q domain; a β-strand
Similar variants
- C1QC p.Ala172Val Uncertain significance ★★ ⚠ same residue
- C1QC p.Gly34Arg Pathogenic ★★ 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-ala172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown