Is APOB p.Arg400His (c.1199G>A) pathogenic?

APOB p.Arg400His (c.1199G>A) is classified Conflicting classifications of pathogenicity in APOB (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2025-12-16). AlphaMissense: likely benign (0.0681); Rare (popmax 0.157%, sas); Associated with familial hypobetalipoproteinemia 1.

What condition is associated with APOB p.Arg400His (c.1199G>A)?

APOB p.Arg400His (c.1199G>A) is associated with familial hypobetalipoproteinemia 1, hypercholesterolemia, autosomal dominant, type B (ClinVar).

How common is APOB p.Arg400His (c.1199G>A) in the general population?

APOB p.Arg400His (c.1199G>A) is rare (popmax 0.157%, sas) (gnomAD).

What do computational predictors say about APOB p.Arg400His (c.1199G>A)?

AlphaMissense predicts likely benign (score 0.0681) — an in-silico prediction, not a clinical call.

APOB p.Arg400His

c.1199G>A · rs530171166 · VCV477795

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0681 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.157%, sas)

Missense predictors

1/2 damaging

AlphaMissense, REVEL

Conditions

familial hypobetalipoproteinemia 1

Computational evidence

Protein change
AlphaMissense	0.0681	likely benign
REVEL	0.664	pathogenic-leaning
⇒ REVEL calls this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.6	GERP -3
Regional constraint	o/e 1.00	unconstrained · MANE · 32 kb · p 0.91 · regional, not allelic
Overall
CADD	8.395	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.157% South Asian · 143/91,078 alleles

Filtering AF 0.136% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.128%

Overall 0.0141% 228/1,614,154 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.157%	637
Middle Eastern	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.008%	12,502
European (non-Finnish)	0.00644%	15,527
Admixed American	0.00167%	60,020
Finnishnot grpmax-eligible	0.00156%	64,012

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.Arg400His
Coding: c.1199G>A
MANE Select: NM_000384
dbSNP: rs530171166
Type: single nucleotide variant
Location: chr2:21032507 (GRCh38)
Gene constraint: LOEUF 0.537 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 400: the vitellogenin domain

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

Disease context

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

Also linked: hypercholesterolemia, autosomal dominant, type B

Similar variants

APOB p.Arg400Cys Conflicting classifications of pathogenicity ★ ⚠ 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
APOB p.Arg2513Ter 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-arg400his (accessed [today's date]).

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