CP p.Cys560Arg
c.1678T>C · VCV3772195
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9712 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
3/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9712 | likely pathogenic ✓ concordant with ClinVar · top 2% in CP |
|---|---|---|
| REVEL | 0.938 | strongly pathogenic-leaning |
| SaProt | LLR -14.38 | damaging |
| ⇒ AlphaMissense, REVEL and SaProt all call this damaging. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
| Regional constraint | o/e 0.80 | unconstrained · MANE · 25 kb · p 2.5e-07 · regional, not allelic |
| Overall | ||
| CADD | 27.4 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- CP
- Protein
- p.Cys560Arg
- Coding
- c.1678T>C
- MANE Select
- NM_000096
- Type
- single nucleotide variant
- Location
- chr3:149198402 (GRCh38)
- Gene constraint
- LOEUF 0.624 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.79 · 4 PDB
- Residue 560
- a β-strand; the plastocyanin-like 3 domain; a disulfide bond
Similar variants
- CP p.Cys560Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
- CP p.Cys560= Likely benign ★ same residue
- CP c.1208+1G>A Pathogenic ★★ same type
- CP c.2879-1G>T Likely pathogenic ★★ same type
- CP p.Arg901Ter Pathogenic ★★ same type
- CP p.Gly195Arg Likely pathogenic ★★ same type
- CP p.Gly650Arg Pathogenic/Likely pathogenic ★★ same type
- CP p.Gly708Ser Pathogenic ★★ 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/cp-p-cys560arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown