Is ABCA2 p.Thr844= (c.2532G>A) pathogenic?

ABCA2 p.Thr844= (c.2532G>A) is classified Likely benign in ABCA2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-28). Ultra-rare (popmax 0.0264%, nfe); Associated with ABCA2-related disorder.

What condition is associated with ABCA2 p.Thr844= (c.2532G>A)?

ABCA2 p.Thr844= (c.2532G>A) is associated with ABCA2-related disorder (ClinVar).

How common is ABCA2 p.Thr844= (c.2532G>A) in the general population?

ABCA2 p.Thr844= (c.2532G>A) is ultra-rare (popmax 0.0264%, nfe) (gnomAD).

ABCA2 p.Thr844=

c.2532G>A · rs566313346 · VCV3040970

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0264%, nfe)

Conditions

ABCA2-related disorder

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 -20	GERP -3.7
Overall
CADD	0.095	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0264% European (non-Finnish) · 312/1,179,892 alleles

Filtering AF 0.024% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.023%

Overall 0.0208% 335/1,612,466 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0264%	3,782
Remaining individualsnot grpmax-eligible	0.024%	4,164
Admixed American	0.00667%	15,001
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,594
African / African-American	0.00267%	37,443
South Asian	0.0011%	91,084

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.Thr844=
Coding: c.2532G>A
MANE Select: NM_001606
dbSNP: rs566313346
Type: single nucleotide variant
Location: chr9:137017217 (GRCh38)
Gene constraint: LOEUF 0.436 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.46
Residue 844: a UniProt-annotated variant site (in idpogsa)

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-thr844 (accessed [today's date]).

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