Is APOC2 p.Glu19Ter (c.55G>T) pathogenic?

APOC2 p.Glu19Ter (c.55G>T) is classified Uncertain significance in APOC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-25). Absent from gnomAD v4.1; Associated with familial apolipoprotein C-II deficiency.

What condition is associated with APOC2 p.Glu19Ter (c.55G>T)?

APOC2 p.Glu19Ter (c.55G>T) is associated with familial apolipoprotein C-II deficiency (ClinVar).

How common is APOC2 p.Glu19Ter (c.55G>T) in the general population?

APOC2 p.Glu19Ter (c.55G>T) is absent from gnomAD v4.1 (gnomAD).

APOC2 p.Glu19Ter

c.55G>T · rs2513572335 · VCV3064990

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

familial apolipoprotein C-II deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 4
Splicing
SpliceAI	Δ0.54	donor loss · deltas
Pangolin	Δ0.58	loss · gain 0.04 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 7.4	GERP 1, phastCons 1
Overall
CADD	47.0	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: APOC2
Protein: p.Glu19Ter
Coding: c.55G>T
MANE Select: NM_000483
dbSNP: rs2513572335
Type: single nucleotide variant
Location: chr19:44948533 (GRCh38)
Gene constraint: LOEUF 1.054 · pLI 0.07 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.81 · 4 PDB

Full APOC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

familial apolipoprotein C-II deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

APOC2 p.Gln92Ter Pathogenic/Likely pathogenic ★★ same condition
APOC2 p.Ala54Asp Uncertain significance ★★ ⚠ same condition
APOC2 p.Ala55Thr Uncertain significance ★★ ⚠ same condition
APOC2 p.Thr23Ile Uncertain significance ★★ ⚠ same condition
APOC2 p.Thr86Arg Uncertain significance ★★ ⚠ same condition
APOC2 c.56-4G>C Benign ★★ same condition
APOC2 p.Glu60Lys Benign/Likely benign ★★ same condition
APOC2 c.216-1G>A 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/apoc2-p-glu19ter (accessed [today's date]).

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