Is ABCB10 p.Thr179= (c.537G>A) pathogenic?

ABCB10 p.Thr179= (c.537G>A) is classified Benign in ABCB10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-01-08). Common (popmax 7.46%, afr) — too common for a highly-penetrant pathogenic allele.

ABCB10 p.Thr179=

Q: How common is ABCB10 p.Thr179= (c.537G>A) in the general population?

ABCB10 p.Thr179= (c.537G>A) is common (popmax 7.46%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.537G>A · rs12080811 · VCV791841

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 7.46%, afr) — too common for a highly-penetrant pathogenic allele

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 -5.9	GERP -3.1
Overall
CADD	0.245	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.46% African / African-American · 5,593/75,002 alleles

Filtering AF 7.29% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.23%

Overall 0.398% 6,416/1,613,886 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.46%	13
Remaining individualsnot grpmax-eligible	0.608%	164
Admixed American	0.485%	206
Middle Eastern	0.413%	242
South Asian	0.0264%	3,794
European (non-Finnish)	0.00873%	11,455

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: ABCB10
Protein: p.Thr179=
Coding: c.537G>A
MANE Select: NM_012089
dbSNP: rs12080811
Type: single nucleotide variant
Location: chr1:229549415 (GRCh38)
Gene constraint: LOEUF 1.142 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.37 · 6 PDB
Residue 179: the abc transmembrane type-1 domain; an α-helix

Full ABCB10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCB10 p.Asn478Lys Benign ★★ same type
ABCB10 p.Ala110Pro Uncertain significance ★ ⚠ same type
ABCB10 p.Ala280Val Uncertain significance ★ ⚠ same type
ABCB10 p.Ala300Pro Uncertain significance ★ ⚠ same type
ABCB10 p.Ala388Gly Uncertain significance ★ ⚠ same type
ABCB10 p.Ala394Thr Uncertain significance ★ ⚠ same type
ABCB10 p.Ala461Val Uncertain significance ★ ⚠ same type
ABCB10 p.Ala503Asp 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/abcb10-p-thr179 (accessed [today's date]).

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