C1R p.Asp142=
c.426C>T · VCV3768294
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.255%, afr)
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 0.82 | GERP 0.8, phastCons 0.73 |
| Overall | ||
| CADD | 10.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.255%
African / African-American · 151/59,266 alleles
Filtering AF
0.222%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.209%
Overall
0.0247%
193/780,678 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.255% | 392 |
| Middle Eastern | 0.045% | 2,221 |
| Admixed American | 0.0237% | 4,217 |
| Remaining individualsnot grpmax-eligible | 0.0171% | 5,864 |
| East Asian | 0.00727% | 13,751 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00409% | 24,450 |
| European (non-Finnish) | 0.00335% | 29,852 |
| South Asian | 0.00268% | 37,301 |
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
- C1R
- Protein
- p.Asp142=
- Coding
- c.426C>T
- MANE Select
- NM_001733
- Type
- single nucleotide variant
- Location
- chr12:7089732 (GRCh38)
- Gene constraint
- LOEUF 0.635 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 87.33 · 12 PDB
- Residue 142
- a binding site; the egf-like; calcium-binding domain
Similar variants
- C1R p.Asp142Glu Uncertain significance ★ ⚠ same residue
- C1R p.Arg301Pro Pathogenic ★★ ⚠ same type
- C1R p.Asp290Gly Pathogenic/Likely pathogenic ★★ same type
- C1R p.Cys338Arg Pathogenic ★★ same type
- C1R p.Cys371Trp Pathogenic ★★ same type
- C1R p.Gly297Asp Pathogenic/Likely pathogenic ★★ same type
- C1R p.His642Gln Uncertain significance ★★ ⚠ same type
- C1R p.Leu285Met 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/c1r-p-asp142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown