Is ABCA9 p.Pro1209Ala (c.3625C>G) pathogenic?

ABCA9 p.Pro1209Ala (c.3625C>G) is classified Uncertain significance in ABCA9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-11). AlphaMissense: ambiguous (0.4113); Very rare (popmax 0.00715%, amr).

How common is ABCA9 p.Pro1209Ala (c.3625C>G) in the general population?

ABCA9 p.Pro1209Ala (c.3625C>G) is very rare (popmax 0.00715%, amr) (gnomAD).

What do computational predictors say about ABCA9 p.Pro1209Ala (c.3625C>G)?

AlphaMissense predicts ambiguous (score 0.4113) — an in-silico prediction, not a clinical call.

ABCA9 p.Pro1209Ala

c.3625C>G · VCV4636043

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4113 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00715%, amr)

Computational evidence

Protein change
AlphaMissense	0.4113	ambiguous
REVEL	0.632	indeterminate
SaProt	LLR -9.95	tolerated
Splicing
SpliceAI	Δ0.30	acceptor gain at this position · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.5	GERP 0.99, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 75 kb · p 0.014 · regional, not allelic
Overall
CADD	22.5	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00715% Admixed American · 4/55,920 alleles

Filtering AF 0.00237% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00142%

Overall 0.000447% 7/1,567,424 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00715%	13,980
East Asian	0.00226%	44,168
African / African-American	0.00136%	73,620
European (non-Finnish)	8.68e-05%	1,151,868

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: ABCA9
Protein: p.Pro1209Ala
Coding: c.3625C>G
MANE Select: NM_080283
Type: single nucleotide variant
Location: chr17:68992266 (GRCh38)
Gene constraint: LOEUF 1.006 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.22

Full ABCA9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCA9 p.Tyr1123= Likely benign ★★ same type
ABCA9 p.Ala1071Val Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1153Thr Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1196Thr Uncertain significance ★ ⚠ same type
ABCA9 p.Ala125Thr Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1285Thr Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1407Val Uncertain significance ★ ⚠ same type
ABCA9 p.Ala1492Pro 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/abca9-p-pro1209ala (accessed [today's date]).

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