Is ABCA2 p.Ala267= (c.801T>G) pathogenic?

ABCA2 p.Ala267= (c.801T>G) is classified Benign in ABCA2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-26). Low-frequency (popmax 2.62%, nfe); Associated with ABCA2-related disorder.

What condition is associated with ABCA2 p.Ala267= (c.801T>G)?

ABCA2 p.Ala267= (c.801T>G) is associated with ABCA2-related disorder (ClinVar).

How common is ABCA2 p.Ala267= (c.801T>G) in the general population?

ABCA2 p.Ala267= (c.801T>G) is low-frequency (popmax 2.62%, nfe) (gnomAD).

ABCA2 p.Ala267=

c.801T>G · rs80138802 · VCV3041634

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 2.62%, nfe)

Conditions

ABCA2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -16	GERP -2.3
Overall
CADD	0.072	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.62% European (non-Finnish) · 30,894/1,179,252 alleles

Filtering AF 2.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.59%

Overall 2.28% 36,790/1,611,188 alleles · low-frequency exomes 34,323/1,458,898 · genomes 2,467/152,290 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	2.62%	38
Finnishnot grpmax-eligible	2.23%	45
Remaining individualsnot grpmax-eligible	2.15%	47
South Asian	1.93%	52
Middle Eastern	1.78%	56
Ashkenazi Jewishnot grpmax-eligible	1.45%	69
Admixed American	1%	100
African / African-American	0.359%	279
East Asian	0.00893%	11,199

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: ABCA2
Protein: p.Ala267=
Coding: c.801T>G
MANE Select: NM_001606
dbSNP: rs80138802
Type: single nucleotide variant
Location: chr9:137021488 (GRCh38)
Gene constraint: LOEUF 0.436 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.46

Full ABCA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ABCA2-related disorder

Similar variants

ABCA2 p.Gln1370Ter Likely pathogenic ★★ same condition
ABCA2 p.Ala1357Thr Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg2392Gln Uncertain significance ★★ ⚠ same condition
ABCA2 p.Glu1515Lys Uncertain significance ★★ ⚠ same condition
ABCA2 p.Ser1427Arg Uncertain significance ★★ ⚠ same condition
ABCA2 p.Arg2298Trp Uncertain significance ★ ⚠ same condition
ABCA2 p.Arg926Trp Uncertain significance ★ ⚠ same condition
ABCA2 p.Thr398Lys Conflicting classifications of pathogenicity ★ ⚠ 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/abca2-p-ala267 (accessed [today's date]).

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