Is ABCB9 p.Asn756= (c.2268C>T) pathogenic?

ABCB9 p.Asn756= (c.2268C>T) is classified Likely benign in ABCB9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-03). Very rare (popmax 0.00456%, sas).

How common is ABCB9 p.Asn756= (c.2268C>T) in the general population?

ABCB9 p.Asn756= (c.2268C>T) is very rare (popmax 0.00456%, sas) (gnomAD).

ABCB9 p.Asn756=

c.2268C>T · VCV3979560

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00456%, 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 -0.016	GERP -3.9, phastCons 0.001
Overall
CADD	5.475	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00456% South Asian · 4/87,734 alleles

Filtering AF 0.00146% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000917%

Overall 0.000846% 12/1,418,180 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00456%	21,933
East Asian	0.00455%	21,964
Remaining individualsnot grpmax-eligible	0.00165%	60,684
European (non-Finnish)	0.000432%	231,448

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.Asn756=
Coding: c.2268C>T
MANE Select: NM_019625
Type: single nucleotide variant
Location: chr12:122929944 (GRCh38)
Gene constraint: LOEUF 0.796 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.76

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

Similar variants

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
ABCB9 p.Ala641Thr Uncertain significance ★ ⚠ same type
ABCB9 p.Ala64Thr 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-asn756 (accessed [today's date]).

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