C1QA p.Ser118=
c.354C>T · rs377376778 · VCV2415754
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0604%, 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 -20 | GERP -3.4 |
| Overall | ||
| CADD | 0.317 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0604%
South Asian · 55/91,058 alleles
Filtering AF
0.0476%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.043%
Overall
0.00545%
88/1,613,960 alleles · ultra-rare
exomes 84/1,461,596 · genomes 4/152,364 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0604% | 1,656 |
| East Asian | 0.0178% | 5,609 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,836 |
| European (non-Finnish) | 0.00186% | 53,631 |
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.Ser118=
- Coding
- c.354C>T
- MANE Select
- NM_015991
- dbSNP
- rs377376778
- Type
- single nucleotide variant
- Location
- chr1:22639023 (GRCh38)
- Gene constraint
- LOEUF 0.997 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 83.68 · 11 PDB
- Residue 118
- the c1q domain; a β-strand
Similar variants
- 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
- C1QA p.Arg44Gln 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-ser118 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown