Is APOC2 p.Asp91fs (c.270del) pathogenic?

APOC2 p.Asp91fs (c.270del) is classified Pathogenic in APOC2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 1988-10-01). No gnomAD frequency available for this variant; Associated with familial apolipoprotein C-II deficiency.

What condition is associated with APOC2 p.Asp91fs (c.270del)?

APOC2 p.Asp91fs (c.270del) is associated with familial apolipoprotein C-II deficiency (ClinVar).

How common is APOC2 p.Asp91fs (c.270del) in the general population?

APOC2 p.Asp91fs (c.270del) is no gnomAD frequency available for this variant (gnomAD).

APOC2 p.Asp91fs

c.270del · rs2122211012 · VCV2576

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

familial apolipoprotein C-II deficiency

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 (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.6	GERP -0.34, 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: APOC2
Protein: p.Asp91fs
Coding: c.270del
MANE Select: NM_000483
dbSNP: rs2122211012
Type: Deletion
Location: chr19:44949213 (GRCh38)
Gene constraint: LOEUF 1.054 · pLI 0.07 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.81 · 4 PDB
Residue 91: the 'lipoprotein lipase cofactor' region

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-asp91fs (accessed [today's date]).

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