CP p.Tyr260=
c.780T>C · rs759309863 · VCV1879596
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.23 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.45 | GERP -3.8 |
| Overall | ||
| CADD | 5.872 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,020 alleles
Overall
6.84e-05%
1/1,461,376 alleles · very rare
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
- CP
- Protein
- p.Tyr260=
- Coding
- c.780T>C
- MANE Select
- NM_000096
- dbSNP
- rs759309863
- Type
- single nucleotide variant
- Location
- chr3:149209212 (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 260
- the plastocyanin-like 2 domain; a β-strand
Similar variants
- 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
- CP p.Leu919Pro Pathogenic/Likely pathogenic ★★ same type
- CP p.Val219Glu Likely 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-tyr260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown