Is CPT2 p.Trp374fs (c.1119_1120del) pathogenic?

CPT2 p.Trp374fs (c.11191120del) is classified Likely pathogenic in CPT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-11-02). Absent from gnomAD.

How common is CPT2 p.Trp374fs (c.1119_1120del) in the general population?

CPT2 p.Trp374fs (c.1119_1120del) is absent from gnomAD (gnomAD).

CPT2 p.Trp374fs

c.1119_1120del · rs2100273567 · VCV1163630

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 5
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.2, phastCons 0.99

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CPT2
Protein: p.Trp374fs
Coding: c.1119_1120del
MANE Select: NM_000098
dbSNP: rs2100273567
Type: Deletion
Location: chr1:53210793 (GRCh38)
Gene constraint: LOEUF 1.038 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.52

Full CPT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CPT2 p.Trp374Ter Likely pathogenic ★ same residue
CPT2 p.Ala643_Leu644insTer Pathogenic/Likely pathogenic ★★ same type
CPT2 p.Arg382fs Pathogenic/Likely pathogenic ★★ same type
CPT2 p.Asp576fs Pathogenic/Likely pathogenic ★★ same type
CPT2 p.Gln33fs Pathogenic ★★ same type
CPT2 p.Glu285fs Pathogenic/Likely pathogenic ★★ same type
CPT2 p.Leu178_Pro180delinsPhe Pathogenic ★★ same type
CPT2 p.Leu556fs 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/cpt2-p-trp374fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown