Is ABCB9 p.Arg717= (c.2151C>T) pathogenic?

ABCB9 p.Arg717= (c.2151C>T) is classified Likely benign in ABCB9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-19). Ultra-rare (popmax 0.0129%, sas).

How common is ABCB9 p.Arg717= (c.2151C>T) in the general population?

ABCB9 p.Arg717= (c.2151C>T) is ultra-rare (popmax 0.0129%, sas) (gnomAD).

ABCB9 p.Arg717=

c.2151C>T · VCV3979341

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0129%, sas)

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 -1.3	GERP -5
Overall
CADD	7.238	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0129% South Asian · 11/85,370 alleles

Filtering AF 0.00719% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00553%

Overall 0.00172% 27/1,568,038 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0129%	7,761
East Asian	0.00706%	14,166
Admixed American	0.0019%	52,652
European (non-Finnish)	0.00104%	96,418

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: ABCB9
Protein: p.Arg717=
Coding: c.2151C>T
MANE Select: NM_019625
Type: single nucleotide variant
Location: chr12:122930061 (GRCh38)
Gene constraint: LOEUF 0.796 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.76
Residue 717: the abc transporter domain

Full ABCB9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCB9 p.Arg717Cys Uncertain significance ★ ⚠ same residue
ABCB9 p.Arg717His Uncertain significance ★ ⚠ same residue
ABCB9 p.Ala151Val Uncertain significance ★ ⚠ same type
ABCB9 p.Ala169Thr Uncertain significance ★ ⚠ same type
ABCB9 p.Ala364Val Uncertain significance ★ ⚠ same type
ABCB9 p.Ala368Val Uncertain significance ★ ⚠ same type
ABCB9 p.Ala447Thr Uncertain significance ★ ⚠ same type
ABCB9 p.Ala641Ser 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/abcb9-p-arg717 (accessed [today's date]).

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