Is COPB2 p.Lys413fs (c.1237_1238del) pathogenic?

COPB2 p.Lys413fs (c.12371238del) is classified Uncertain significance in COPB2 (ClinVar, Single submitter, 2 submitters; last evaluated 2021-11-30). No gnomAD frequency available for this variant; Associated with COPB2-related disorder.

What condition is associated with COPB2 p.Lys413fs (c.1237_1238del)?

COPB2 p.Lys413fs (c.1237_1238del) is associated with COPB2-related disorder, osteoporosis, childhood- or juvenile-onset, with developmental delay (ClinVar).

How common is COPB2 p.Lys413fs (c.1237_1238del) in the general population?

COPB2 p.Lys413fs (c.1237_1238del) is no gnomAD frequency available for this variant (gnomAD).

COPB2 p.Lys413fs

c.1237_1238del · rs2107801839 · VCV1327119

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

COPB2-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 in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 11 of 22
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.8	GERP -1.3, 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: COPB2
Protein: p.Lys413fs
Coding: c.1237_1238del
MANE Select: NM_004766
dbSNP: rs2107801839
Type: Deletion
Location: chr3:139369512 (GRCh38)
Gene constraint: LOEUF 0.177 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 86.75 · 2 PDB
Residue 413: a β-strand

Full COPB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

COPB2-related disorder

Also linked: osteoporosis, childhood- or juvenile-onset, with developmental delay

Similar variants

COPB2 p.Val222fs Conflicting classifications of pathogenicity ★ ⚠ same condition
COPB2 c.229-10_229-9del Likely benign same condition
COPB2 c.1401+2T>A Likely pathogenic ★ same condition
COPB2 p.Glu493fs Likely pathogenic ★ same condition
COPB2 p.His556fs Likely pathogenic ★ same condition
COPB2 p.Val83fs Pathogenic ★ same condition
COPB2 c.751+4A>G Uncertain significance ★ same condition
COPB2 p.Leu439Ser Uncertain significance ★ ⚠ 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/copb2-p-lys413fs (accessed [today's date]).

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