Is ABCC2 p.Asp620Glu (c.1860T>A) pathogenic?

ABCC2 p.Asp620Glu (c.1860T>A) is classified Uncertain significance in ABCC2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-03-25). AlphaMissense: likely benign (0.1202); Rare (popmax 0.138%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ABCC2 p.Asp620Glu (c.1860T>A)?

ABCC2 p.Asp620Glu (c.1860T>A) is associated with Inborn genetic diseases, Dubin-Johnson syndrome (ClinVar).

How common is ABCC2 p.Asp620Glu (c.1860T>A) in the general population?

ABCC2 p.Asp620Glu (c.1860T>A) is rare (popmax 0.138%, nfe) (gnomAD).

What do computational predictors say about ABCC2 p.Asp620Glu (c.1860T>A)?

AlphaMissense predicts likely benign (score 0.1202) — an in-silico prediction, not a clinical call.

ABCC2 p.Asp620Glu

c.1860T>A · rs141413284 · VCV298454

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.1202 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.138%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1202	likely benign
REVEL	0.13	moderately benign-leaning
SaProt	LLR -5.66	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3	GERP -5.1
Regional constraint	o/e 0.98	unconstrained · MANE · 69 kb · p 0.48 · regional, not allelic
Overall
CADD	2.461	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.138% European (non-Finnish) · 1,629/1,179,612 alleles

Filtering AF 0.132% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.13%

Overall 0.109% 1,755/1,613,660 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.138%	724
Admixed American	0.102%	984
Remaining individualsnot grpmax-eligible	0.0672%	1,488
African / African-American	0.0293%	3,410
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,588

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.Asp620Glu
Coding: c.1860T>A
MANE Select: NM_000392
dbSNP: rs141413284
Type: single nucleotide variant
Location: chr10:99810178 (GRCh38)
Gene constraint: LOEUF 0.985 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.40 · 16 PDB
Residue 620: an α-helix

Full ABCC2 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

Also linked: Dubin-Johnson syndrome

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-asp620glu (accessed [today's date]).

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