Is ABCA1 p.Arg1068= (c.3204C>T) pathogenic?

ABCA1 p.Arg1068= (c.3204C>T) is classified Benign/Likely benign in ABCA1 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-01-27). Rare (popmax 0.629%, sas); Associated with Cardiovascular phenotype.

What condition is associated with ABCA1 p.Arg1068= (c.3204C>T)?

ABCA1 p.Arg1068= (c.3204C>T) is associated with Cardiovascular phenotype, Tangier disease, hypoalphalipoproteinemia, primary, 1 (ClinVar).

How common is ABCA1 p.Arg1068= (c.3204C>T) in the general population?

ABCA1 p.Arg1068= (c.3204C>T) is rare (popmax 0.629%, sas) (gnomAD).

ABCA1 p.Arg1068=

c.3204C>T · rs55814314 · VCV364420

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

rare (popmax 0.629%, sas)

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 0.077	GERP -0.72, phastCons 0.61
Overall
CADD	7.904	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.629% South Asian · 573/91,088 alleles

Filtering AF 0.586% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.57%

Overall 0.0828% 1,337/1,614,204 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.629%	159
Middle Eastern	0.544%	184
Remaining individualsnot grpmax-eligible	0.0672%	1,488
European (non-Finnish)	0.0552%	1,813
Admixed American	0.05%	2,001
African / African-American	0.00933%	10,720
East Asian	0.00223%	44,882

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.Arg1068=
Coding: c.3204C>T
MANE Select: NM_005502
dbSNP: rs55814314
Type: single nucleotide variant
Location: chr9:104819623 (GRCh38)
Gene constraint: LOEUF 0.563 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.50 · 7 PDB
Residue 1068: the abc transporter 1 domain; an α-helix; a UniProt-annotated variant site (in tgd)

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

Similar variants

ABCA1 p.Arg1068Gly Uncertain significance ★ ⚠ same residue
ABCA1 c.4175+1G>T Pathogenic/Likely pathogenic ★★ same condition
ABCA1 c.5237+3A>C Likely pathogenic ★★ same condition
ABCA1 p.Arg2080Trp Likely pathogenic ★★ same condition
ABCA1 p.Arg587Trp Pathogenic/Likely pathogenic ★★ same condition
ABCA1 p.Asn1800His Pathogenic/Likely pathogenic ★★ ⚠ same condition
ABCA1 p.Thr940Met Pathogenic/Likely pathogenic ★★ same condition
ABCA1 c.3787+5C>A 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-arg1068 (accessed [today's date]).

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