Is ABCB1 p.Leu662= (c.1984C>T) pathogenic?

ABCB1 p.Leu662= (c.1984C>T) is classified Likely benign in ABCB1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-23). Ultra-rare (popmax 0.044%, afr); Associated with ABCB1-related disorder.

What condition is associated with ABCB1 p.Leu662= (c.1984C>T)?

ABCB1 p.Leu662= (c.1984C>T) is associated with ABCB1-related disorder (ClinVar).

How common is ABCB1 p.Leu662= (c.1984C>T) in the general population?

ABCB1 p.Leu662= (c.1984C>T) is ultra-rare (popmax 0.044%, afr) (gnomAD).

ABCB1 p.Leu662=

c.1984C>T · rs138422716 · VCV3039097

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.044%, afr)

Conditions

ABCB1-related disorder

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 1.5	GERP -0.12, phastCons 1
Overall
CADD	6.724	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.044% African / African-American · 33/75,030 alleles

Filtering AF 0.0321% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0281%

Overall 0.00291% 47/1,614,024 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.044%	2,274
Admixed American	0.0183%	5,456
Remaining individualsnot grpmax-eligible	0.0048%	20,833

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: ABCB1
Protein: p.Leu662=
Coding: c.1984C>T
MANE Select: NM_001348946
dbSNP: rs138422716
Type: single nucleotide variant
Location: chr7:87544903 (GRCh38)
Gene constraint: LOEUF 0.575 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.72 · 24 PDB
Residue 662: the 'disordered' region

Full ABCB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ABCB1-related disorder

Similar variants

ABCB1 p.Ile849Thr Uncertain significance ⚠ same condition
ABCB1 c.1887+4T>G Likely benign same condition
ABCB1 c.2397+8T>A Likely benign same condition
ABCB1 c.2786+9C>T Likely benign same condition
ABCB1 c.338+5T>C Likely benign same condition
ABCB1 c.702+9A>T Likely benign same condition
ABCB1 c.-43A>G Benign same condition
ABCB1 p.Phe204= Likely benign 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/abcb1-p-leu662 (accessed [today's date]).

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