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NM_000033.4(ABCD1):c.1628C>T (p.Pro543Leu)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Nov 19, 2021)
Last evaluated:
Mar 31, 2020
Accession:
VCV000528341.5
Variation ID:
528341
Description:
single nucleotide variant
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NM_000033.4(ABCD1):c.1628C>T (p.Pro543Leu)

Allele ID
534632
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 153740231 (GRCh38) GRCh38 UCSC
X: 153005685 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_1017:g.20364C>T
LRG_1017t1:c.1628C>T LRG_1017p1:p.Pro543Leu
NC_000023.10:g.153005685C>T
... more HGVS
Protein change
P543L
Other names
-
Canonical SPDI
NC_000023.11:153740230:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00000
Links
ClinGen: CA415112044
dbSNP: rs1557054776
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Mar 31, 2020 RCV000727694.5
Pathogenic 1 criteria provided, single submitter Aug 20, 2018 RCV000633485.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ABCD1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
739 965

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 25, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000855037.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(May 16, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000883320.1
Submitted: (Oct 10, 2018)
Evidence details
Comment:
The ABCD1 c.1628C>T; p.Pro543Leu variant has been described in several individuals affected with adrenoleukodystrophy (ALD) with no detectable level of peroxisomal ABC half-transporter (ALDP) in … (more)
Pathogenic
(Aug 20, 2018)
criteria provided, single submitter
Method: clinical testing
Adrenoleukodystrophy
Allele origin: germline
Invitae
Accession: SCV000754718.3
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (9)
Comment:
This sequence change replaces proline with leucine at codon 543 of the ABCD1 protein (p.Pro543Leu). The proline residue is highly conserved and there is a … (more)
Likely pathogenic
(Mar 31, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001475502.1
Submitted: (Dec 30, 2020)
Evidence details
Publications
PubMed (10)
Comment:
Not found in the total gnomAD dataset, and the data is high quality. Predicted to have a damaging effect on the protein. Found in multiple … (more)
Pathogenic
(Sep 28, 2021)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002022866.1
Submitted: (Nov 19, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Pathogenicity of novel ABCD1 variants: The need for biochemical testing in the era of advanced genetics. Schackmann MJ Molecular genetics and metabolism 2016 PMID: 27067449
Molecular analysis in X-linked adrenoleukodystrophy patients: identification of a novel mutation. Durmaz A Metabolic brain disease 2014 PMID: 24788897
X-linked adrenoleukodystrophy in women: a cross-sectional cohort study. Engelen M Brain : a journal of neurology 2014 PMID: 24480483
Glutathione imbalance in patients with X-linked adrenoleukodystrophy. Petrillo S Molecular genetics and metabolism 2013 PMID: 23768953
Adrenomyeloneuropathy in patients with 'Addison's disease': genetic case analysis. Mukherjee S Journal of the Royal Society of Medicine 2006 PMID: 16672758
X-linked adrenoleukodystrophy in Spain. Identification of 26 novel mutations in the ABCD1 gene in 80 patients. Improvement of genetic counseling in 162 relative females. Coll MJ Clinical genetics 2005 PMID: 15811009
ABCD1 mutations and the X-linked adrenoleukodystrophy mutation database: role in diagnosis and clinical correlations. Kemp S Human mutation 2001 PMID: 11748843
Detection of mutations in the ALD gene (ABCD1) in seven Italian families: description of four novel mutations. Lira MG Human mutation 2000 PMID: 10980539
Determination of 30 X-linked adrenoleukodystrophy mutations, including 15 not previously described. Lachtermacher MB Human mutation 2000 PMID: 10737980
Variability of endocrinological dysfunction in 55 patients with X-linked adrenoleucodystrophy: clinical, laboratory and genetic findings. Korenke GC European journal of endocrinology 1997 PMID: 9242200
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ABCD1 - - - -

Text-mined citations for rs1557054776...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 28, 2021