CPT2 p.Lys274Ter
c.820A>T · VCV4973909
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
CPT2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 5 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 36.0 | 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
- CPT2
- Protein
- p.Lys274Ter
- Coding
- c.820A>T
- MANE Select
- NM_000098
- Type
- single nucleotide variant
- Location
- chr1:53210494 (GRCh38)
- Gene constraint
- LOEUF 1.038 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.52
Disease context
CPT2-related disorder
Similar variants
- CPT2 p.Lys274Arg Uncertain significance ★★ ⚠ same residue
- CPT2 p.Lys274= Likely benign ★ same residue
- CPT2 c.340+1G>C Pathogenic/Likely pathogenic ★★ same condition
- CPT2 p.Arg124Gln Likely pathogenic ★★ ⚠ same condition
- CPT2 p.Arg124Ter Pathogenic/Likely pathogenic ★★ same condition
- CPT2 p.Arg151Trp Pathogenic ★★ same condition
- CPT2 p.Arg503Cys Pathogenic/Likely pathogenic ★★ same condition
- CPT2 p.Arg631Cys Pathogenic ★★ ⚠ same condition
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/cpt2-p-lys274ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown