Is ABCD1 p.Val86= (c.258C>T) pathogenic?

ABCD1 p.Val86= (c.258C>T) is classified Benign/Likely benign in ABCD1 (ClinVar, Multiple submitters, 15 submitters; last evaluated 2026-01-31). Rare (popmax 0.151%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ABCD1 p.Val86= (c.258C>T)?

ABCD1 p.Val86= (c.258C>T) is associated with Inborn genetic diseases, adrenoleukodystrophy (ClinVar).

How common is ABCD1 p.Val86= (c.258C>T) in the general population?

ABCD1 p.Val86= (c.258C>T) is rare (popmax 0.151%, nfe) (gnomAD).

ABCD1 p.Val86=

c.258C>T · rs200660869 · VCV368045

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 15 submitters

gnomAD v4.1

Rare

rare (popmax 0.151%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.25	GERP -2.5, phastCons 0.51
Overall
CADD	6.164	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.151% European (non-Finnish) · 1,319/873,767 alleles

Filtering AF 0.144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.141%

Overall 0.124% 1,449/1,168,449 alleles · rare exomes 1,377/1,055,153 · genomes 72/113,296 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.151%	662
Remaining individualsnot grpmax-eligible	0.135%	739
Finnishnot grpmax-eligible	0.11%	911
African / African-American	0.0246%	4,060
South Asian	0.0078%	12,822
Admixed American	0.00713%	14,029
Ashkenazi Jewishnot grpmax-eligible	0.00497%	20,101

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.Val86=
Coding: c.258C>T
MANE Select: NM_000033
dbSNP: rs200660869
Type: single nucleotide variant
Location: chrX:153725524 (GRCh38)
Structure: AlphaFold pLDDT 81.58 · 14 PDB
Residue 86: a β-strand; the 'interaction with pex19' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: adrenoleukodystrophy

Similar variants

ABCD1 p.Val86Asp Uncertain significance ★ ⚠ 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
ABCD1 c.1866-1G>C Likely pathogenic ★★ same condition
ABCD1 c.1866-2A>T Likely pathogenic ★★ same condition
ABCD1 c.901-1G>A 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-val86 (accessed [today's date]).

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