CP p.Ala649=
c.1947C>T · rs749108953 · VCV1879595
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00659%, sas)
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 1.5 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 12.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00659%
South Asian · 6/91,084 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.00161%
26/1,613,934 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00659% | 15,181 |
| East Asian | 0.00445% | 22,449 |
| African / African-American | 0.00401% | 24,964 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
| European (non-Finnish) | 0.0011% | 90,769 |
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.Ala649=
- Coding
- c.1947C>T
- MANE Select
- NM_000096
- dbSNP
- rs749108953
- Type
- single nucleotide variant
- Location
- chr3:149186650 (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 649
- the plastocyanin-like 4 domain; a disulfide bond
Similar variants
- CP p.Ala649Thr Benign/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
- CP p.Leu919Pro Pathogenic/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-ala649 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown