C1QA p.Leu13=
c.39G>C · rs138830154 · VCV1107925
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.019 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 0.46, phastCons 1 |
| Overall | ||
| CADD | 9.381 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
African / African-American · 20/74,918 alleles
Filtering AF
0.0177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00136%
22/1,613,980 alleles · ultra-rare
exomes 14/1,461,814 · genomes 8/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0267% | 3,746 |
| Admixed American | 0.00167% | 59,996 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
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.Leu13=
- Coding
- c.39G>C
- MANE Select
- NM_015991
- dbSNP
- rs138830154
- Type
- single nucleotide variant
- Location
- chr1:22637655 (GRCh38)
- Gene constraint
- LOEUF 0.997 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 83.68 · 11 PDB
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-leu13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown