Is CEBPA p.Pro115fs (c.342_343insATGA) pathogenic?

CEBPA p.Pro115fs (c.342343insATGA) is classified Likely pathogenic in CEBPA (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-22). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with CEBPA p.Pro115fs (c.342_343insATGA)?

CEBPA p.Pro115fs (c.342_343insATGA) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CEBPA p.Pro115fs (c.342_343insATGA) in the general population?

CEBPA p.Pro115fs (c.342_343insATGA) is absent from gnomAD (gnomAD).

CEBPA p.Pro115fs

c.342_343insATGA · rs2145262824 · VCV1692807

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

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (1 of 1) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.2	GERP -2.5, 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: CEBPA
Protein: p.Pro115fs
Coding: c.342_343insATGA
MANE Select: NM_004364
dbSNP: rs2145262824
Type: Insertion
Location: chr19:33302072 (GRCh38)
Gene constraint: LOEUF 1.372 · pLI 0.26 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 2 PDB

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEBPA p.Pro115Leu Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro115Ser Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro115= Likely benign ★★ same residue
CEBPA p.191HP[2] Uncertain significance ★★ same condition
CEBPA p.191HP[5] Uncertain significance ★★ same condition
CEBPA p.Gln88Arg Uncertain significance ★★ ⚠ same condition
CEBPA p.Gly122Ala Uncertain significance ★★ ⚠ same condition
CEBPA p.His18Tyr 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/cebpa-p-pro115fs (accessed [today's date]).

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