Is ABCA12 p.Asp1930Val (c.5789A>T) pathogenic?

ABCA12 p.Asp1930Val (c.5789A>T) is classified Uncertain significance in ABCA12 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-02). AlphaMissense: likely pathogenic (0.6251); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ABCA12 p.Asp1930Val (c.5789A>T)?

ABCA12 p.Asp1930Val (c.5789A>T) is associated with Inborn genetic diseases (ClinVar).

How common is ABCA12 p.Asp1930Val (c.5789A>T) in the general population?

ABCA12 p.Asp1930Val (c.5789A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABCA12 p.Asp1930Val (c.5789A>T)?

AlphaMissense predicts likely pathogenic (score 0.6251) — an in-silico prediction, not a clinical call.

ABCA12 p.Asp1930Val

c.5789A>T · VCV4840765

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6251 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6251	likely pathogenic
REVEL	0.892	moderately pathogenic-leaning
SaProt	LLR -6.33	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 7.9	GERP 2, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 85 kb · p 1.7e-09 · regional, not allelic
Overall
CADD	26.8	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ABCA12
Protein: p.Asp1930Val
Coding: c.5789A>T
MANE Select: NM_173076
Type: single nucleotide variant
Location: chr2:214966943 (GRCh38)
Gene constraint: LOEUF 0.582 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32
Residue 1930: 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.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
ABCA12 p.Asp756Val Uncertain significance ★★ ⚠ same condition
ABCA12 p.Gly2305Arg 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-asp1930val (accessed [today's date]).

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