Is ABCD1 p.Pro560= (c.1680G>A) pathogenic?

ABCD1 p.Pro560= (c.1680G>A) is classified Likely benign in ABCD1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-24). Very rare (popmax 0.00525%, afr); Associated with adrenoleukodystrophy.

What condition is associated with ABCD1 p.Pro560= (c.1680G>A)?

ABCD1 p.Pro560= (c.1680G>A) is associated with adrenoleukodystrophy (ClinVar).

How common is ABCD1 p.Pro560= (c.1680G>A) in the general population?

ABCD1 p.Pro560= (c.1680G>A) is very rare (popmax 0.00525%, afr) (gnomAD).

How is X-linked adrenoleukodystrophy inherited?

Typically X-linked dominant (Orphanet). A genetic counselor can assess individual risk for a family.

ABCD1 p.Pro560=

c.1680G>A · rs782005164 · VCV1136035

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00525%, afr)

Conditions

adrenoleukodystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP -13	GERP -3.8
Overall
CADD	0.244	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00525% African / African-American · 3/57,105 alleles

Filtering AF 0.00139% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000686%

Overall 0.000993% 12/1,208,340 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00525%	19,035
European (non-Finnish)	0.00101%	99,447

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: ABCD1
Protein: p.Pro560=
Coding: c.1680G>A
MANE Select: NM_000033
dbSNP: rs782005164
Type: single nucleotide variant
Location: chrX:153740619 (GRCh38)
Structure: AlphaFold pLDDT 81.58 · 14 PDB
Residue 560: a UniProt-annotated variant site (in ald; cald-type); a UniProt-annotated variant site (in ald; amn and almd-types); a UniProt-annotated variant site (in ald); a turn; the abc transporter domain

Full ABCD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

adrenoleukodystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked adrenoleukodystrophy (Orphanet):

Inheritance: X-linked dominant
Onset: Adolescent, Adult, Childhood, Elderly
Prevalence: 1-9 / 1 000 000 (Israel)

Similar variants

ABCD1 p.Pro560Leu Pathogenic ★★ same residue
ABCD1 p.Pro560Arg Likely pathogenic ★ same residue
ABCD1 p.Pro560Ser Likely pathogenic ★ same residue
ABCD1 p.Pro560Thr Likely pathogenic ★ same residue
ABCD1 c.1635-2A>G Pathogenic ★★ same condition
ABCD1 c.1781-1G>C Pathogenic ★★ same condition
ABCD1 c.1781-1G>T Pathogenic/Likely pathogenic ★★ same condition
ABCD1 c.1866-10G>A Pathogenic/Likely pathogenic ★★ same condition

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/abcd1-p-pro560 (accessed [today's date]).

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