CP p.Ser121Ter
c.362C>A · VCV4964661
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
CP-related disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 19 |
| Splicing | ||
| SpliceAI | Δ0.23 | donor loss, 32 bp away · masked 0 · deltas |
| Pangolin | Δ0.32 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 6.6 | GERP 0.24, phastCons 1 |
| Overall | ||
| CADD | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Ser121Ter
- Coding
- c.362C>A
- MANE Select
- NM_000096
- Type
- single nucleotide variant
- Location
- chr3:149212483 (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 121
- the plastocyanin-like 1 domain; a β-strand
Disease context
CP-related disorders
Similar variants
- CP p.Trp230Ter Pathogenic ★ same condition
- CP p.Trp644Ter Likely pathogenic ★ same condition
- CP p.Lys753Ter Likely pathogenic same condition
- CP p.Tyr1011Ter Pathogenic same condition
- CP p.Val996Ala Uncertain significance ⚠ same condition
- CP p.Cys13= Likely benign same condition
- CP p.Glu380fs Likely pathogenic ★ same condition
- CP c.1208+1G>A 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-ser121ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown