Is APOB p.Arg490= (c.1468C>A) pathogenic?

APOB p.Arg490= (c.1468C>A) is classified Likely benign in APOB (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-18). Ultra-rare (popmax 0.0117%, amr); Associated with Cardiovascular phenotype.

What condition is associated with APOB p.Arg490= (c.1468C>A)?

APOB p.Arg490= (c.1468C>A) is associated with Cardiovascular phenotype, hypercholesterolemia, autosomal dominant, type B, familial hypobetalipoproteinemia 1 (ClinVar).

How common is APOB p.Arg490= (c.1468C>A) in the general population?

APOB p.Arg490= (c.1468C>A) is ultra-rare (popmax 0.0117%, amr) (gnomAD).

APOB p.Arg490=

c.1468C>A · rs771541567 · VCV1122261

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0117%, amr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>A here scores Δ0.98 · evaluated, not missing
Constraint at this position
Conservation	phyloP 4.4	GERP -1, phastCons 1
Overall
CADD	16.44	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0117% Admixed American · 7/59,992 alleles

Filtering AF 0.00543% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.000745% 12/1,610,642 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0117%	8,570
Remaining individualsnot grpmax-eligible	0.0016%	62,370
European (non-Finnish)	0.00034%	294,320

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: APOB
Protein: p.Arg490=
Coding: c.1468C>A
MANE Select: NM_000384
dbSNP: rs771541567
Type: single nucleotide variant
Location: chr2:21029900 (GRCh38)
Gene constraint: LOEUF 0.537 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 490: the vitellogenin domain; a disulfide bond; a UniProt-annotated variant site (in fhbl1; reduced protein secretion)

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hypercholesterolemia, autosomal dominant, type B familial hypobetalipoproteinemia 1

Similar variants

APOB p.Arg490Trp Pathogenic/Likely pathogenic ★★ same residue
APOB p.Arg490Gln Uncertain significance ★★ same residue
APOB c.1830-1G>A Pathogenic ★★ same condition
APOB c.2604+1G>A Likely pathogenic ★★ same condition
APOB c.537+1G>T Pathogenic/Likely pathogenic ★★ same condition
APOB p.Arg1333Ter Pathogenic ★★ same condition
APOB p.Arg2012Ter Pathogenic ★★ same condition
APOB p.Arg2085Ter Pathogenic/Likely 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/apob-p-arg490 (accessed [today's date]).

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