Is ABCA2 p.Val1154Met (c.3460G>A) pathogenic?

ABCA2 p.Val1154Met (c.3460G>A) is classified Uncertain significance in ABCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-28). AlphaMissense: likely pathogenic (0.8575); Ultra-rare (popmax 0.0111%, eas).

How common is ABCA2 p.Val1154Met (c.3460G>A) in the general population?

ABCA2 p.Val1154Met (c.3460G>A) is ultra-rare (popmax 0.0111%, eas) (gnomAD).

What do computational predictors say about ABCA2 p.Val1154Met (c.3460G>A)?

AlphaMissense predicts likely pathogenic (score 0.8575) — an in-silico prediction, not a clinical call.

ABCA2 p.Val1154Met

c.3460G>A · rs376990200 · VCV2540496

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8575 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0111%, eas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8575	likely pathogenic
REVEL	0.764	pathogenic-leaning
SaProt	LLR -5.22	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 0.56, phastCons 1
Regional constraint	o/e 0.59	unconstrained · MANE · 914 bp · p 3.8e-13 · regional, not allelic
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM V1153M vs ClinVar V1154M) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0111% East Asian · 5/44,862 alleles

Filtering AF 0.00435% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00276%

Overall 0.00124% 20/1,611,688 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0111%	8,972
African / African-American	0.00534%	18,734
South Asian	0.0022%	45,520
Remaining individualsnot grpmax-eligible	0.0016%	62,442
European (non-Finnish)	0.000678%	147,452

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.Val1154Met
Coding: c.3460G>A
MANE Select: NM_001606
dbSNP: rs376990200
Type: single nucleotide variant
Location: chr9:137015729 (GRCh38)
Gene constraint: LOEUF 0.436 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.46
Residue 1154: the abc transporter 1 domain; a UniProt-annotated variant site (in idpogsa)

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

Similar variants

ABCA2 p.Gln1370Ter Likely pathogenic ★★ same type
ABCA2 c.3883-3C>T Uncertain significance ★★ same type
ABCA2 p.Ala1357Thr Uncertain significance ★★ ⚠ same type
ABCA2 p.Ala1620Thr Uncertain significance ★★ ⚠ same type
ABCA2 p.Ala1645Val Uncertain significance ★★ ⚠ same type
ABCA2 p.Ala1715Ser Uncertain significance ★★ ⚠ same type
ABCA2 p.Ala2180Thr Uncertain significance ★★ ⚠ same type
ABCA2 p.Ala2206Val Uncertain significance ★★ ⚠ same type

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-val1154met (accessed [today's date]).

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