Is ABCC2 p.Ala985= (c.2955G>A) pathogenic?

ABCC2 p.Ala985= (c.2955G>A) is classified Conflicting classifications of pathogenicity in ABCC2 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-27). Ultra-rare (popmax 0.092%, afr); Associated with Dubin-Johnson syndrome.

What condition is associated with ABCC2 p.Ala985= (c.2955G>A)?

ABCC2 p.Ala985= (c.2955G>A) is associated with Dubin-Johnson syndrome (ClinVar).

How common is ABCC2 p.Ala985= (c.2955G>A) in the general population?

ABCC2 p.Ala985= (c.2955G>A) is ultra-rare (popmax 0.092%, afr) (gnomAD).

How is Dubin-Johnson syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ABCC2 p.Ala985=

c.2955G>A · rs139082536 · VCV498612

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.092%, afr)

Conditions

Dubin-Johnson syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.4	GERP -4.6
Overall
CADD	5.264	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.092% African / African-American · 69/75,034 alleles

Filtering AF 0.0745% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0682%

Overall 0.0297% 479/1,614,176 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.092%	1,087
Remaining individualsnot grpmax-eligible	0.0848%	1,179
European (non-Finnish)	0.0285%	3,512
Admixed American	0.0117%	8,575
East Asian	0.0111%	8,978
Finnishnot grpmax-eligible	0.0109%	9,147
South Asian	0.0022%	45,545

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: ABCC2
Protein: p.Ala985=
Coding: c.2955G>A
MANE Select: NM_000392
dbSNP: rs139082536
Type: single nucleotide variant
Location: chr10:99831682 (GRCh38)
Gene constraint: LOEUF 0.985 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.40 · 16 PDB
Residue 985: an α-helix; the abc transmembrane type-1 2 domain

Full ABCC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Dubin-Johnson syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Dubin-Johnson syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult

Similar variants

ABCC2 c.1031+4A>G Pathogenic/Likely pathogenic ★★ same condition
ABCC2 c.3258+1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCC2 c.333+1G>A Likely pathogenic ★★ same condition
ABCC2 c.3415-1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCC2 c.3741+1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCC2 c.3741+1G>T Pathogenic/Likely pathogenic ★★ same condition
ABCC2 c.576+1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCC2 p.Arg1066Ter 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/abcc2-p-ala985 (accessed [today's date]).

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