Is APOB p.Ala10= (c.30G>C) pathogenic?

APOB p.Ala10= (c.30G>C) is classified Likely benign in APOB (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-06-19). Very rare (popmax 9.21e-05%, nfe); Associated with familial hypobetalipoproteinemia 1.

What condition is associated with APOB p.Ala10= (c.30G>C)?

APOB p.Ala10= (c.30G>C) is associated with familial hypobetalipoproteinemia 1, hypercholesterolemia, autosomal dominant, type B (ClinVar).

How common is APOB p.Ala10= (c.30G>C) in the general population?

APOB p.Ala10= (c.30G>C) is very rare (popmax 9.21e-05%, nfe) (gnomAD).

APOB p.Ala10=

c.30G>C · rs985120737 · VCV1727626

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 9.21e-05%, nfe)

Conditions

familial hypobetalipoproteinemia 1

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.071	GERP 0.59, phastCons 0.1
Overall
CADD	8.78	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 9.21e-05% European (non-Finnish) · 1/1,085,422 alleles

Overall 7.08e-05% 1/1,411,598 alleles · very rare exomes 1/1,259,634 · genomes 0/151,964 · joint denominator

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.Ala10=
Coding: c.30G>C
MANE Select: NM_000384
dbSNP: rs985120737
Type: single nucleotide variant
Location: chr2:21043916 (GRCh38)

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

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-ala10 (accessed [today's date]).

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