Is CP p.Glu380fs (c.1139_1148del) pathogenic?

CP p.Glu380fs (c.11391148del) is classified Likely pathogenic in CP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-29). Absent from gnomAD; Associated with CP-related disorder.

What condition is associated with CP p.Glu380fs (c.1139_1148del)?

CP p.Glu380fs (c.1139_1148del) is associated with CP-related disorder (ClinVar).

How common is CP p.Glu380fs (c.1139_1148del) in the general population?

CP p.Glu380fs (c.1139_1148del) is absent from gnomAD (gnomAD).

CP p.Glu380fs

c.1139_1148del · rs2472840199 · VCV2631312

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

Conditions

CP-related disorder

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 6 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 2.2, phastCons 1

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: CP
Protein: p.Glu380fs
Coding: c.1139_1148del
MANE Select: NM_000096
dbSNP: rs2472840199
Type: Deletion
Location: chr3:149206228 (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 380: a β-strand; the plastocyanin-like 3 domain

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

Disease context

CP-related disorder

Similar variants

CP p.Ser121Ter Likely pathogenic ★ same condition
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 c.607+1del 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-glu380fs (accessed [today's date]).

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