Is ABCB7 p.Cys289= (c.867C>T) pathogenic?

ABCB7 p.Cys289= (c.867C>T) is classified Likely benign in ABCB7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-01). Very rare (popmax 0.00593%, eas).

How common is ABCB7 p.Cys289= (c.867C>T) in the general population?

ABCB7 p.Cys289= (c.867C>T) is very rare (popmax 0.00593%, eas) (gnomAD).

ABCB7 p.Cys289=

c.867C>T · rs769487666 · VCV2660940

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00593%, eas)

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 -0.42	GERP -3.5
Overall
CADD	3.905	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00593% East Asian · 2/33,714 alleles

Filtering AF 0.00418% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0037%

Overall 0.00474% 57/1,203,359 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00593%	16,857
European (non-Finnish)	0.0054%	18,525
Remaining individualsnot grpmax-eligible	0.00422%	23,693
South Asian	0.00353%	28,323
African / African-American	0.0035%	28,580
Admixed American	0.00219%	45,690

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: ABCB7
Protein: p.Cys289=
Coding: c.867C>T
MANE Select: NM_001271696
dbSNP: rs769487666
Type: single nucleotide variant
Location: chrX:75073945 (GRCh38)
Structure: AlphaFold pLDDT 78.19 · 4 PDB
Residue 289: the abc transmembrane type-1 domain

Full ABCB7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCB7 c.1659+5T>G Uncertain significance ★★ same type
ABCB7 c.1935+5G>C Uncertain significance ★★ same type
ABCB7 p.Ala5Glu Uncertain significance ★★ ⚠ same type
ABCB7 p.Arg711His Uncertain significance ★★ ⚠ same type
ABCB7 p.Asn378Asp Uncertain significance ★★ ⚠ same type
ABCB7 p.Asp653Asn Uncertain significance ★★ ⚠ same type
ABCB7 p.Glu494Gln Uncertain significance ★★ ⚠ same type
ABCB7 p.Gly197Cys 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/abcb7-p-cys289 (accessed [today's date]).

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