Is ABCA1 p.Pro2150= (c.6450G>A) pathogenic?

ABCA1 p.Pro2150= (c.6450G>A) is classified Benign/Likely benign in ABCA1 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-01). Low-frequency (popmax 3.8%, afr); Associated with Cardiovascular phenotype.

What condition is associated with ABCA1 p.Pro2150= (c.6450G>A)?

ABCA1 p.Pro2150= (c.6450G>A) is associated with Cardiovascular phenotype, Tangier disease, hypoalphalipoproteinemia, primary, 1 (ClinVar).

How common is ABCA1 p.Pro2150= (c.6450G>A) in the general population?

ABCA1 p.Pro2150= (c.6450G>A) is low-frequency (popmax 3.8%, afr) (gnomAD).

ABCA1 p.Pro2150=

c.6450G>A · rs61741359 · VCV364378

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.8%, afr)

Conditions

Cardiovascular phenotype

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 0.021	GERP -4.2, phastCons 0.036
Overall
CADD	9.624	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.8% African / African-American · 2,852/75,016 alleles

Filtering AF 3.69% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.64%

Overall 0.2% 3,226/1,614,088 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.8%	26
Admixed American	0.305%	328
Remaining individualsnot grpmax-eligible	0.214%	466
Middle Eastern	0.116%	866
South Asian	0.0121%	8,278
European (non-Finnish)	0.00331%	30,257

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: ABCA1
Protein: p.Pro2150=
Coding: c.6450G>A
MANE Select: NM_018376 · reported on NM_005502
dbSNP: rs61741359
Type: single nucleotide variant
Location: chr9:104785591 (GRCh38)

Full ABCA1 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

Also linked: Tangier disease hypoalphalipoproteinemia, primary, 1

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-pro2150 (accessed [today's date]).

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