NM_000033.4(ABCD1):c.1695del (p.Asp565fs) AND Adrenoleukodystrophy

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 6, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001235149.6

Allele description [Variation Report for NM_000033.4(ABCD1):c.1695del (p.Asp565fs)]

NM_000033.4(ABCD1):c.1695del (p.Asp565fs)

Gene:

ABCD1:ATP binding cassette subfamily D member 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_000033.4(ABCD1):c.1695del (p.Asp565fs)

HGVS:

NC_000023.11:g.153740634del
NG_009022.2:g.20767del
NM_000033.4:c.1695delMANE SELECT
NP_000024.2:p.Asp565fs
LRG_1017t1:c.1695del
LRG_1017:g.20767del
LRG_1017p1:p.Asp565fs
NC_000023.10:g.153006088del
NM_000033.3:c.1695del

Protein change:

D565fs

Links:

dbSNP: rs2091764622

NCBI 1000 Genomes Browser:

rs2091764622

Molecular consequence:

NM_000033.4:c.1695del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Adrenoleukodystrophy (ALD)
Synonyms:: ADDISON DISEASE AND CEREBRAL SCLEROSIS; BRONZE SCHILDER DISEASE; MELANODERMIC LEUKODYSTROPHY; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018544; MedGen: C0162309; OMIM: 300100

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Nucleotide Links for Gene (Select 162333) (54)
Nucleotide
Oryza meyeriana var. granulata linkage group LG12 Lachesis_group11__82_contigs__...
Oryza meyeriana var. granulata linkage group LG12 Lachesis_group11__82_contigs__length_35419118, whole genome shotgun sequence
gi|1796536887|gb|SPHZ02000004.1||gn :SPHZ02|Lachesis_group11__82_contigs__length_35419118

Nucleotide
probable E3 ubiquitin-protein ligase MARCHF10 isoform 3 [Homo sapiens]
probable E3 ubiquitin-protein ligase MARCHF10 isoform 3 [Homo sapiens]
gi|571026626|ref|NP_001275709.1|

Protein
PREDICTED: Homo sapiens membrane associated ring-CH-type finger 10 (MARCHF10), t...
PREDICTED: Homo sapiens membrane associated ring-CH-type finger 10 (MARCHF10), transcript variant X2, mRNA
gi|2217310350|ref|XM_005257096.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001407821	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 6, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11748843, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001407821

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 6, 2020)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ABCD1 mutations and the X-linked adrenoleukodystrophy mutation database: role in diagnosis and clinical correlations.

Kemp S, Pujol A, Waterham HR, van Geel BM, Boehm CD, Raymond GV, Cutting GR, Wanders RJ, Moser HW.

Hum Mutat. 2001 Dec;18(6):499-515. Review.

PubMed [citation]

PMID:: 11748843

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001407821.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in ABCD1 are known to be pathogenic (PMID: 11748843). This variant has not been reported in the literature in individuals with ABCD1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Asp565Glufs*71) in the ABCD1 gene. It is expected to result in an absent or disrupted protein product.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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