Is APOB p.Asn1531fs (c.4590del) pathogenic?

APOB p.Asn1531fs (c.4590del) is classified Pathogenic in APOB (ClinVar, Single submitter, 1 submitter; last evaluated 2016-03-01). Absent from gnomAD; Associated with hypercholesterolemia, familial, 1.

What condition is associated with APOB p.Asn1531fs (c.4590del)?

APOB p.Asn1531fs (c.4590del) is associated with hypercholesterolemia, familial, 1 (ClinVar).

How common is APOB p.Asn1531fs (c.4590del) in the general population?

APOB p.Asn1531fs (c.4590del) is absent from gnomAD (gnomAD).

APOB p.Asn1531fs

c.4590del · rs1135402765 · VCV431498

Pathogenic Single submitter

Classification

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

hypercholesterolemia, familial, 1

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 haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 26 of 29
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.2	GERP 1.7, 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: APOB
Protein: p.Asn1531fs
Coding: c.4590del
MANE Select: NM_000384
dbSNP: rs1135402765
Type: Deletion
Location: chr2:21012278 (GRCh38)
Gene constraint: LOEUF 0.537 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)

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

Disease context

hypercholesterolemia, familial, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

APOB p.Asn1531His Uncertain significance ★★ same residue
APOB c.12088-13del Benign ★★ same condition
APOB p.Gln2383fs Likely pathogenic ★ same condition
APOB p.Glu1004fs Pathogenic ★ same condition
APOB p.Glu4387fs Pathogenic ★ same condition
APOB p.Leu14fs Pathogenic ★ same condition
APOB p.Thr170fs Likely pathogenic ★ same condition
APOB p.Ala13_Leu14del 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/apob-p-asn1531fs (accessed [today's date]).

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