Is ABCA1 p.Phe2009Ser (c.6026T>C) pathogenic?

ABCA1 p.Phe2009Ser (c.6026T>C) is classified Pathogenic in ABCA1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2002-05-21). AlphaMissense: likely pathogenic (0.9873); Absent from gnomAD v4.1; Associated with hypoalphalipoproteinemia, primary, 1.

What condition is associated with ABCA1 p.Phe2009Ser (c.6026T>C)?

ABCA1 p.Phe2009Ser (c.6026T>C) is associated with hypoalphalipoproteinemia, primary, 1 (ClinVar).

How common is ABCA1 p.Phe2009Ser (c.6026T>C) in the general population?

ABCA1 p.Phe2009Ser (c.6026T>C) is absent from gnomAD v4.1 (gnomAD).

How is Apolipoprotein A-I deficiency inherited?

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

What do computational predictors say about ABCA1 p.Phe2009Ser (c.6026T>C)?

AlphaMissense predicts likely pathogenic (score 0.9873) — an in-silico prediction, not a clinical call.

ABCA1 p.Phe2009Ser

c.6026T>C · rs137854499 · VCV9502

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9873 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hypoalphalipoproteinemia, primary, 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
AlphaMissense	0.9873	likely pathogenic ✓ concordant with ClinVar
REVEL	0.933	strongly pathogenic-leaning
SaProt	LLR -11.85	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 11	GERP 2, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 22 kb · p 3.8e-10 · regional, not allelic
Overall
CADD	28.7	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: ABCA1
Protein: p.Phe2009Ser
Coding: c.6026T>C
MANE Select: NM_005502
dbSNP: rs137854499
Type: single nucleotide variant
Location: chr9:104788469 (GRCh38)

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

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-phe2009ser (accessed [today's date]).

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