Is ABCC9 p.Val1007Ala (c.3020T>C) pathogenic?

ABCC9 p.Val1007Ala (c.3020T>C) is classified Uncertain significance in ABCC9 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-06-17). AlphaMissense: ambiguous (0.5277); Absent from gnomAD v4.1.

How common is ABCC9 p.Val1007Ala (c.3020T>C) in the general population?

ABCC9 p.Val1007Ala (c.3020T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABCC9 p.Val1007Ala (c.3020T>C)?

AlphaMissense predicts ambiguous (score 0.5277) — an in-silico prediction, not a clinical call.

ABCC9 p.Val1007Ala

c.3020T>C · VCV3372357

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.5277 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.5277	ambiguous
REVEL	0.38	indeterminate
SaProt	LLR -9.61	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1
Regional constraint	o/e 0.56	unconstrained · MANE · 1,230 bp · p 3.5e-07 · regional, not allelic
Overall
CADD	23.1	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: ABCC9
Protein: p.Val1007Ala
Coding: c.3020T>C
MANE Select: NM_020297
Type: single nucleotide variant
Location: chr12:21845679 (GRCh38)
Gene constraint: LOEUF 0.557 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.72
Residue 1007: the abc transmembrane type-1 2 domain

Full ABCC9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCC9 p.Val1007Leu Uncertain significance ★ same residue
ABCC9 p.Val1007= Likely benign ★ same residue
ABCC9 c.2506-1G>A Pathogenic/Likely pathogenic ★★ same type
ABCC9 p.Arg1116Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
ABCC9 p.Arg1116His Pathogenic ★★ ⚠ same type
ABCC9 p.Arg1154Gln Pathogenic ★★ ⚠ same type
ABCC9 p.Arg1154Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
ABCC9 p.Gln852Ter Pathogenic/Likely pathogenic ★★ 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/abcc9-p-val1007ala (accessed [today's date]).

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