Is ABCC9 p.Asp793Val (c.2378A>T) pathogenic?

ABCC9 p.Asp793Val (c.2378A>T) is classified Likely pathogenic in ABCC9 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-01-29). AlphaMissense: likely pathogenic (0.9967); Absent from gnomAD v4.1.

How common is ABCC9 p.Asp793Val (c.2378A>T) in the general population?

ABCC9 p.Asp793Val (c.2378A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABCC9 p.Asp793Val (c.2378A>T)?

AlphaMissense predicts likely pathogenic (score 0.9967) — an in-silico prediction, not a clinical call.

ABCC9 p.Asp793Val

c.2378A>T · rs1057521640 · VCV383474

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9967 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9967	likely pathogenic ✓ concordant with ClinVar · top 5% in ABCC9
REVEL	0.935	strongly pathogenic-leaning
SaProt	LLR -12.81	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>C here scores Δ0.34 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, phastCons 1
Regional constraint	o/e 0.39	unconstrained · MANE · 8,585 bp · p 7.2e-08 · regional, not allelic
Overall
CADD	28.4	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.Asp793Val
Coding: c.2378A>T
MANE Select: NM_020297
dbSNP: rs1057521640
Type: single nucleotide variant
Location: chr12:21861017 (GRCh38)
Gene constraint: LOEUF 0.557 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.72
Residue 793: the abc transporter 1 domain

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

Similar variants

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
ABCC9 p.Gly989Glu Pathogenic/Likely pathogenic ★★ same type
ABCC9 p.Thr1202Met 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-asp793val (accessed [today's date]).

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