C1QA p.Lys103=
c.309G>A · rs759712266 · VCV1561486
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00755%, 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 1.7 | GERP -0.63, phastCons 1 |
| Overall | ||
| CADD | 3.883 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00755%
European (non-Finnish) · 89/1,178,744 alleles
Filtering AF
0.00624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00577%
93/1,611,356 alleles · very rare
exomes 92/1,459,098 · genomes 1/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00755% | 13,244 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,593 |
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
- C1QA
- Protein
- p.Lys103=
- Coding
- c.309G>A
- MANE Select
- NM_015991
- dbSNP
- rs759712266
- Type
- single nucleotide variant
- Location
- chr1:22638978 (GRCh38)
- Gene constraint
- LOEUF 0.997 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 83.68 · 11 PDB
- Residue 103
- the collagen-like domain; the 'disordered' region
Similar variants
- C1QA p.Lys103fs Pathogenic ★ same residue
- C1QA p.Arg27Ter Pathogenic/Likely pathogenic ★★ same type
- C1QA p.Gln208Ter Pathogenic ★★ same type
- C1QA p.Gly157Asp Likely pathogenic ★★ same type
- C1QA p.Arg150Gln Uncertain significance ★★ ⚠ same type
- C1QA p.Arg180Lys Uncertain significance ★★ ⚠ same type
- C1QA p.Arg27Gln Uncertain significance ★★ ⚠ same type
- C1QA p.Arg42Gln 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/c1qa-p-lys103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown