Is APOB p.Phe3779Leu (c.11337T>G) pathogenic?

APOB p.Phe3779Leu (c.11337T>G) is classified Uncertain significance in APOB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-02). AlphaMissense: likely pathogenic (0.8709); Absent from gnomAD v4.1.

How common is APOB p.Phe3779Leu (c.11337T>G) in the general population?

APOB p.Phe3779Leu (c.11337T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APOB p.Phe3779Leu (c.11337T>G)?

AlphaMissense predicts likely pathogenic (score 0.8709) — an in-silico prediction, not a clinical call.

APOB p.Phe3779Leu

c.11337T>G · VCV4536490

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8709 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.8709	likely pathogenic · top 1% in APOB
REVEL	0.099	moderately benign-leaning
⇒ AlphaMissense calls this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP 0.43, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 9,629 bp · p 0.051 · regional, not allelic
Overall
CADD	20.6	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: APOB
Protein: p.Phe3779Leu
Coding: c.11337T>G
MANE Select: NM_000384
Type: single nucleotide variant
Location: chr2:21005531 (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

Similar variants

APOB c.1830-1G>A Pathogenic ★★ same type
APOB c.2604+1G>A Likely pathogenic ★★ same type
APOB c.537+1G>T Pathogenic/Likely pathogenic ★★ same type
APOB p.Arg1333Ter Pathogenic ★★ same type
APOB p.Arg2012Ter Pathogenic ★★ same type
APOB p.Arg2085Ter Pathogenic/Likely pathogenic ★★ same type
APOB p.Arg2513Ter Pathogenic ★★ same type
APOB p.Arg2520Ter Pathogenic/Likely pathogenic ★★ same type

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-phe3779leu (accessed [today's date]).

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