Is ABCG2 p.Met71Val (c.211A>G) pathogenic?

ABCG2 p.Met71Val (c.211A>G) is classified Likely benign in ABCG2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-01). AlphaMissense: ambiguous (0.4125); Rare (popmax 0.379%, mid).

How common is ABCG2 p.Met71Val (c.211A>G) in the general population?

ABCG2 p.Met71Val (c.211A>G) is rare (popmax 0.379%, mid) (gnomAD).

What do computational predictors say about ABCG2 p.Met71Val (c.211A>G)?

AlphaMissense predicts ambiguous (score 0.4125) — an in-silico prediction, not a clinical call.

ABCG2 p.Met71Val

c.211A>G · VCV4533545

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4125 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.379%, mid)

Computational evidence

Protein change
AlphaMissense	0.4125	ambiguous
REVEL	0.602	indeterminate
SaProt	LLR -9.31	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.7, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 48 kb · p 0.73 · regional, not allelic
Overall
CADD	24.9	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

Grpmax group 0.379% Middle Eastern · 23/6,062 alleles

Filtering AF 0.259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.22%

Overall 0.0727% 1,173/1,614,198 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.379%	264
South Asian	0.152%	660
Admixed American	0.085%	1,177
Remaining individualsnot grpmax-eligible	0.0784%	1,276
European (non-Finnish)	0.0749%	1,335
Ashkenazi Jewishnot grpmax-eligible	0.0405%	2,467
Finnishnot grpmax-eligible	0.0156%	6,404
African / African-American	0.00799%	12,510

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: ABCG2
Protein: p.Met71Val
Coding: c.211A>G
MANE Select: NM_004827
Type: single nucleotide variant
Location: chr4:88132628 (GRCh38)
Gene constraint: LOEUF 1.308 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.54 · 29 PDB
Residue 71: the abc transporter domain; a β-strand

Full ABCG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCG2 p.Tyr123= Benign ★★ same type
ABCG2 p.Ala505Gly Uncertain significance ★ ⚠ same type
ABCG2 p.Arg575Gln Uncertain significance ★ ⚠ same type
ABCG2 p.Asn289Lys Uncertain significance ★ ⚠ same type
ABCG2 p.Asp312Gly Uncertain significance ★ ⚠ same type
ABCG2 p.Asp419Tyr Uncertain significance ★ ⚠ same type
ABCG2 p.Gln324His Uncertain significance ★ ⚠ same type
ABCG2 p.Gln393Arg Uncertain significance ★ ⚠ 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/abcg2-p-met71val (accessed [today's date]).

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