Is ABCA1 p.Val916fs (c.2745_2754del) pathogenic?

ABCA1 p.Val916fs (c.27452754del) is classified Likely pathogenic in ABCA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-01). Associated with hypoalphalipoproteinemia, primary, 1.

What condition is associated with ABCA1 p.Val916fs (c.2745_2754del)?

ABCA1 p.Val916fs (c.2745_2754del) is associated with hypoalphalipoproteinemia, primary, 1 (ClinVar).

How is Apolipoprotein A-I deficiency inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

ABCA1 p.Val916fs

c.2745_2754del · VCV3779318

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

hypoalphalipoproteinemia, primary, 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 19 of 50
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.4	GERP -3.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: ABCA1
Protein: p.Val916fs
Coding: c.2745_2754del
MANE Select: NM_005502
Type: Deletion
Location: chr9:104822570 (GRCh38)
Gene constraint: LOEUF 0.563 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.50 · 7 PDB
Residue 916: the abc transporter 1 domain

Full ABCA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For Apolipoprotein A-I deficiency (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages

Similar variants

ABCA1 p.Val916= Benign/Likely benign ★★ same residue
ABCA1 p.Pro1284fs Pathogenic same condition
ABCA1 c.5237+3A>C Likely pathogenic ★★ same condition
ABCA1 p.Asn1800His Pathogenic/Likely pathogenic ★★ ⚠ same condition
ABCA1 c.*2330A>T Uncertain significance ★★ same condition
ABCA1 c.*379C>T Uncertain significance ★★ same condition
ABCA1 p.Arg126Cys Uncertain significance ★★ ⚠ same condition
ABCA1 p.Arg1342Trp 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/abca1-p-val916fs (accessed [today's date]).

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