Is ABCB1 p.Arg157Gln (c.470G>A) pathogenic?

ABCB1 p.Arg157Gln (c.470G>A) is classified Uncertain significance in ABCB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-11). AlphaMissense: likely benign (0.1004); Ultra-rare (popmax 0.0167%, amr); Associated with inflammatory bowel disease 13.

What condition is associated with ABCB1 p.Arg157Gln (c.470G>A)?

ABCB1 p.Arg157Gln (c.470G>A) is associated with inflammatory bowel disease 13 (ClinVar).

How common is ABCB1 p.Arg157Gln (c.470G>A) in the general population?

ABCB1 p.Arg157Gln (c.470G>A) is ultra-rare (popmax 0.0167%, amr) (gnomAD).

What do computational predictors say about ABCB1 p.Arg157Gln (c.470G>A)?

AlphaMissense predicts likely benign (score 0.1004) — an in-silico prediction, not a clinical call.

ABCB1 p.Arg157Gln

c.470G>A · rs202002337 · VCV1032492

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1004 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0167%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

inflammatory bowel disease 13

Computational evidence

Protein change
AlphaMissense	0.1004	likely benign
REVEL	0.265	benign-leaning
SaProt	LLR -8.33	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 -0.48	GERP 0.027
Regional constraint	o/e 0.85	unconstrained · MANE · 96 kb · p 6.7e-09 · regional, not allelic
Overall
CADD	8.646	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 0.0167% Admixed American · 10/60,018 alleles

Filtering AF 0.009% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00681%

Overall 0.00217% 35/1,614,120 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0167%	6,002
East Asian	0.00223%	44,886
European (non-Finnish)	0.00186%	53,638
Remaining individualsnot grpmax-eligible	0.0016%	62,506
African / African-American	0.00133%	75,014

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.Arg157Gln
Coding: c.470G>A
MANE Select: NM_001348946
dbSNP: rs202002337
Type: single nucleotide variant
Location: chr7:87566845 (GRCh38)
Gene constraint: LOEUF 0.575 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.72 · 24 PDB
Residue 157: the abc transmembrane type-1 1 domain

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

Disease context

inflammatory bowel disease 13 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCB1 p.Ser893Ala Benign ★★ same condition
ABCB1 p.Arg1183Cys Uncertain significance ★ ⚠ same condition
ABCB1 p.Ile160Met Uncertain significance ★ ⚠ same condition
ABCB1 p.Ser2Cys Uncertain significance ★ same condition
ABCB1 c.287-25G>T Benign ★★ same type
ABCB1 p.Ala1132= Benign/Likely benign ★★ same type
ABCB1 p.Gln1107Pro Benign/Likely benign ★★ same type
ABCB1 p.Glu243= Benign/Likely benign ★★ 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/abcb1-p-arg157gln (accessed [today's date]).

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