Is ABCD1 p.Ser514= (c.1542C>T) pathogenic?

ABCD1 p.Ser514= (c.1542C>T) is classified Likely benign in ABCD1 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-08-16). Very rare (popmax 0.00218%, amr); Associated with adrenoleukodystrophy.

What condition is associated with ABCD1 p.Ser514= (c.1542C>T)?

ABCD1 p.Ser514= (c.1542C>T) is associated with adrenoleukodystrophy (ClinVar).

How common is ABCD1 p.Ser514= (c.1542C>T) in the general population?

ABCD1 p.Ser514= (c.1542C>T) is very rare (popmax 0.00218%, amr) (gnomAD).

How is X-linked adrenoleukodystrophy inherited?

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

ABCD1 p.Ser514=

c.1542C>T · rs149643908 · VCV1144379

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00218%, amr)

Conditions

adrenoleukodystrophy

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.341	indeterminate
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.35	GERP -2.3, phastCons 0.12
Overall
CADD	5.448	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00218% Admixed American · 1/45,898 alleles

Filtering AF 0.000474% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000343%

Overall 0.000827% 10/1,209,419 alleles · very rare exomes 9/1,096,436 · genomes 1/112,983 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00218%	45,898
European (non-Finnish)	0.00101%	99,353

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.Ser514=
Coding: c.1542C>T
MANE Select: NM_000033
dbSNP: rs149643908
Type: single nucleotide variant
Location: chrX:153740145 (GRCh38)

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)

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-ser514 (accessed [today's date]).

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