NC_000023.10:g.(?_153001546)_(154563736_?)dup AND Adrenoleukodystrophy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 16, 2022
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:: RCV003119108.3

Allele description [Variation Report for NC_000023.10:g.(?_153001546)_(154563736_?)dup]

NC_000023.10:g.(?_153001546)_(154563736_?)dup

Genes:

ABCD1:ATP binding cassette subfamily D member 1 [Gene - OMIM - HGNC]
ATP6AP1:ATPase H+ transporting accessory protein 1 [Gene - OMIM - HGNC]
BRCC3:BRCA1/BRCA2-containing complex subunit 3 [Gene - OMIM - HGNC]
CMC4:C-X9-C motif containing 4 [Gene - OMIM - HGNC]
FAM3A:FAM3 metabolism regulating signaling molecule A [Gene - OMIM - HGNC]
FUNDC2:FUN14 domain containing 2 [Gene - OMIM - HGNC]
GDI1:GDP dissociation inhibitor 1 [Gene - OMIM - HGNC]
GAB3:GRB2 associated binding protein 3 [Gene - OMIM - HGNC]
H2AB1:H2A.B variant histone 1 [Gene - OMIM - HGNC]
LAGE3:L antigen family member 3 [Gene - OMIM - HGNC]
L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]
MPP1:MAGUK p55 scaffold protein 1 [Gene - OMIM - HGNC]
NAA10:N-alpha-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
PDZD4:PDZ domain containing 4 [Gene - OMIM - HGNC]
RAB39B:RAB39B, member RAS oncogene family [Gene - OMIM - HGNC]
ARHGAP4:Rho GTPase activating protein 4 [Gene - OMIM - HGNC]
SRPK3:SRSF protein kinase 3 [Gene - OMIM - HGNC]
VBP1:VHL binding protein 1 [Gene - OMIM - HGNC]
AVPR2:arginine vasopressin receptor 2 [Gene - OMIM - HGNC]
CTAG1A:cancer/testis antigen 1A [Gene - OMIM - HGNC]
CTAG1B:cancer/testis antigen 1B [Gene - OMIM - HGNC]
CTAG2:cancer/testis antigen 2 [Gene - OMIM - HGNC]
CLIC2:chloride intracellular channel 2 [Gene - OMIM - HGNC]
F8A1:coagulation factor VIII associated 1 [Gene - OMIM - HGNC]
F8:coagulation factor VIII [Gene - OMIM - HGNC]
DNASE1L1:deoxyribonuclease 1 like 1 [Gene - OMIM - HGNC]
DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]
EMD:emerin [Gene - OMIM - HGNC]
FAM50A:family with sequence similarity 50 member A [Gene - OMIM - HGNC]
FLNA:filamin A [Gene - OMIM - HGNC]
G6PD:glucose-6-phosphate dehydrogenase [Gene - OMIM - HGNC]
HCFC1:host cell factor C1 [Gene - OMIM - HGNC]
IKBKG:inhibitor of nuclear factor kappa B kinase regulatory subunit gamma [Gene - OMIM - HGNC]
IRAK1:interleukin 1 receptor associated kinase 1 [Gene - OMIM - HGNC]
IDH3G:isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [Gene - OMIM - HGNC]
MTCP1:mature T cell proliferation 1 [Gene - OMIM - HGNC]
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
OPN1LW:opsin 1, long wave sensitive [Gene - OMIM - HGNC]
OPN1MW2:opsin 1, medium wave sensitive 2 [Gene - HGNC]
OPN1MW:opsin 1, medium wave sensitive [Gene - OMIM - HGNC]
PLXNA3:plexin A3 [Gene - OMIM - HGNC]
PLXNB3:plexin B3 [Gene - OMIM - HGNC]
RENBP:renin binding protein [Gene - OMIM - HGNC]
RPL10:ribosomal protein L10 [Gene - OMIM - HGNC]
SSR4:signal sequence receptor subunit 4 [Gene - OMIM - HGNC]
SMIM9:small integral membrane protein 9 [Gene - HGNC]
SLC10A3:solute carrier family 10 member 3 [Gene - OMIM - HGNC]
TAFAZZIN:tafazzin, phospholipid-lysophospholipid transacylase [Gene - OMIM - HGNC]
TEX28:testis expressed 28 [Gene - OMIM - HGNC]
TKTL1:transketolase like 1 [Gene - OMIM - HGNC]
TMEM187:transmembrane protein 187 [Gene - OMIM - HGNC]
UBL4A:ubiquitin like 4A [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xq28

Genomic location:

ChrX: 153001546 - 154563736 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_153001546)_(154563736_?)dup

HGVS:

NC_000023.10:g.(?_153001546)_(154563736_?)dup

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

Recent activity

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Escherichia coli strain E-D 371 EC1678_c85, whole genome shotgun sequence
Escherichia coli strain E-D 371 EC1678_c85, whole genome shotgun sequence
gi|1035742185|ref|NZ_LFHV01000085.1 |WGS:NZ_LFHV01|EC1678_c85

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003790067	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 16, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003790067

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 16, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

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 Invitae, SCV003790067.2

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

Description

This variant results in a copy number gain of the genomic region encompassing exon(s) 3-10 of the ABCD1 gene. This region includes the termination codon of the gene. This copy number gain extends beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with ABCD1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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 8, 2024

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