C1R p.Cys89=
c.267T>C · VCV4847170
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.64 | GERP -3.4, phastCons 0.9 |
| Overall | ||
| CADD | 3.439 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- C1R
- Protein
- p.Cys89=
- Coding
- c.267T>C
- MANE Select
- NM_001733
- Type
- single nucleotide variant
- Location
- chr12:7090213 (GRCh38)
- Gene constraint
- LOEUF 0.635 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 87.33 · 12 PDB
- Residue 89
- a disulfide bond; the cub 1 domain
Similar variants
- C1R p.Cys89Arg Likely pathogenic 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-cys89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown