Is ABCA12 p.Pro534Ala (c.1600C>G) pathogenic?

ABCA12 p.Pro534Ala (c.1600C>G) is classified Conflicting classifications of pathogenicity in ABCA12 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-02-06). AlphaMissense: likely benign (0.2232); Ultra-rare (popmax 0.0571%, sas); Associated with Inborn genetic diseases.

What condition is associated with ABCA12 p.Pro534Ala (c.1600C>G)?

ABCA12 p.Pro534Ala (c.1600C>G) is associated with Inborn genetic diseases (ClinVar).

How common is ABCA12 p.Pro534Ala (c.1600C>G) in the general population?

ABCA12 p.Pro534Ala (c.1600C>G) is ultra-rare (popmax 0.0571%, sas) (gnomAD).

What do computational predictors say about ABCA12 p.Pro534Ala (c.1600C>G)?

AlphaMissense predicts likely benign (score 0.2232) — an in-silico prediction, not a clinical call.

ABCA12 p.Pro534Ala

c.1600C>G · rs557461059 · VCV3021190

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2232 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0571%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2232	likely benign
REVEL	0.097	moderately benign-leaning
SaProt	LLR -7.31	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.4, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 94 kb · p 0.48 · regional, not allelic
Overall
CADD	12.04	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 0.0571% South Asian · 52/91,042 alleles

Filtering AF 0.0447% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0403%

Overall 0.00335% 54/1,613,482 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0571%	1,751
Remaining individualsnot grpmax-eligible	0.0032%	31,221

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: ABCA12
Protein: p.Pro534Ala
Coding: c.1600C>G
MANE Select: NM_173076
dbSNP: rs557461059
Type: single nucleotide variant
Location: chr2:215019393 (GRCh38)
Gene constraint: LOEUF 0.582 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32
Residue 534: a UniProt-annotated variant site (in arci4b)

Full ABCA12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCA12 p.Pro534Leu Likely benign ★ same residue
ABCA12 p.Pro534= Likely benign ★ same residue
ABCA12 p.Ala134Ser Uncertain significance ★★ ⚠ same condition
ABCA12 p.Ala51Glu Uncertain significance ★★ ⚠ same condition
ABCA12 p.Ala833Val Uncertain significance ★★ ⚠ same condition
ABCA12 p.Arg1417Trp Uncertain significance ★★ ⚠ same condition
ABCA12 p.Arg1950Gln Uncertain significance ★★ ⚠ same condition
ABCA12 p.Asp505Val 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/abca12-p-pro534ala (accessed [today's date]).

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