C1QA p.Ser178=
c.534C>T · rs368473383 · VCV1164575
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.46%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.012 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -3.7 |
| Overall | ||
| CADD | 1.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.46%
South Asian · 1,329/91,092 alleles
Filtering AF
1.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.37%
Overall
0.0908%
1,466/1,614,264 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.46% | 69 |
| Remaining individualsnot grpmax-eligible | 0.101% | 992 |
| Middle Eastern | 0.066% | 1,516 |
| European (non-Finnish) | 0.00576% | 17,353 |
| Admixed American | 0.00167% | 60,036 |
| African / African-American | 0.00133% | 75,076 |
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.Ser178=
- Coding
- c.534C>T
- MANE Select
- NM_015991
- dbSNP
- rs368473383
- Type
- single nucleotide variant
- Location
- chr1:22639203 (GRCh38)
- Gene constraint
- LOEUF 0.997 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 83.68 · 11 PDB
- Residue 178
- the c1q domain; a β-strand
Similar variants
- C1QA p.Ser178Phe Uncertain significance ★★ ⚠ 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-ser178 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown