Is APOB p.His3239= (c.9717C>T) pathogenic?

APOB p.His3239= (c.9717C>T) is classified Likely benign in APOB (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-28). Very rare (popmax 0.00167%, amr); Associated with Cardiovascular phenotype.

What condition is associated with APOB p.His3239= (c.9717C>T)?

APOB p.His3239= (c.9717C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is APOB p.His3239= (c.9717C>T) in the general population?

APOB p.His3239= (c.9717C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

APOB p.His3239=

c.9717C>T · rs150668826 · VCV927814

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.2	GERP -2, phastCons 0.23
Overall
CADD	2.471	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,942 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.00062% 10/1,613,804 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,942
African / African-American	0.00134%	74,896
South Asian	0.0011%	91,084
European (non-Finnish)	0.000593%	168,561

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.His3239=
Coding: c.9717C>T
MANE Select: NM_000384
dbSNP: rs150668826
Type: single nucleotide variant
Location: chr2:21007151 (GRCh38)
Gene constraint: LOEUF 0.537 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 3239: a disulfide bond

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

Similar variants

APOB p.His3239Tyr Conflicting classifications of pathogenicity ★ ⚠ same residue
APOB p.His3239Arg Uncertain significance ★ ⚠ same residue
APOB p.Arg490Trp Pathogenic/Likely pathogenic ★★ same condition
APOB c.1124+3A>G Uncertain significance ★★ same condition
APOB c.11788+4A>G Uncertain significance ★★ same condition
APOB c.12087+2T>C Uncertain significance ★★ same condition
APOB p.Ala1320Thr Uncertain significance ★★ ⚠ same condition
APOB p.Ala1695Val 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-his3239 (accessed [today's date]).

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