Is ABCB4 p.Asn902Asp (c.2704A>G) pathogenic?

ABCB4 p.Asn902Asp (c.2704A>G) is classified Uncertain significance in ABCB4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-04-14). AlphaMissense: ambiguous (0.5545); Absent from gnomAD v4.1; Associated with ABCB4-related disorder.

What condition is associated with ABCB4 p.Asn902Asp (c.2704A>G)?

ABCB4 p.Asn902Asp (c.2704A>G) is associated with ABCB4-related disorder, familial intrahepatic cholestasis (ClinVar).

How common is ABCB4 p.Asn902Asp (c.2704A>G) in the general population?

ABCB4 p.Asn902Asp (c.2704A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABCB4 p.Asn902Asp (c.2704A>G)?

AlphaMissense predicts ambiguous (score 0.5545) — an in-silico prediction, not a clinical call.

ABCB4 p.Asn902Asp

c.2704A>G · rs2546763879 · VCV2637025

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.5545 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

ABCB4-related disorder

Computational evidence

Protein change
AlphaMissense	0.5545	ambiguous
REVEL	0.882	moderately pathogenic-leaning
SaProt	LLR -12.42	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	Δ0.48	acceptor gain, 21 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 14 kb · p 8.2e-06 · regional, not allelic
Overall
CADD	27.2	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: ABCB4
Protein: p.Asn902Asp
Coding: c.2704A>G
MANE Select: NM_000443
dbSNP: rs2546763879
Type: single nucleotide variant
Location: chr7:87413696 (GRCh38)
Gene constraint: LOEUF 0.623 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 83.36 · 4 PDB
Residue 902: the abc transmembrane type-1 2 domain

Full ABCB4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ABCB4-related disorder

Also linked: familial intrahepatic cholestasis

Similar variants

ABCB4 c.2064+3A>T Likely pathogenic ★★ same condition
ABCB4 c.2211+1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCB4 c.2682+1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCB4 c.2783+1G>T Pathogenic/Likely pathogenic ★★ same condition
ABCB4 c.286+1G>A Pathogenic ★★ same condition
ABCB4 c.3081+1G>C Pathogenic ★★ same condition
ABCB4 c.3486+1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCB4 c.3486+1G>T Pathogenic/Likely pathogenic ★★ 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/abcb4-p-asn902asp (accessed [today's date]).

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