GRCh38/hg38 Xp11.4-11.3(chrX:41823849-44240337)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 12, 2011
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:: RCV000053092.5

Allele description [Variation Report for GRCh38/hg38 Xp11.4-11.3(chrX:41823849-44240337)x1]

GRCh38/hg38 Xp11.4-11.3(chrX:41823849-44240337)x1

Genes:

LOC130068175:ATAC-STARR-seq lymphoblastoid active region 29562 [Gene]
LOC130068172:ATAC-STARR-seq lymphoblastoid silent region 20778 [Gene]
LOC130068173:ATAC-STARR-seq lymphoblastoid silent region 20779 [Gene]
LOC130068174:ATAC-STARR-seq lymphoblastoid silent region 20780 [Gene]
LOC130068176:ATAC-STARR-seq lymphoblastoid silent region 20781 [Gene]
LOC130068177:ATAC-STARR-seq lymphoblastoid silent region 20782 [Gene]
EFHC2:EF-hand domain containing 2 [Gene - OMIM - HGNC]
LOC126863241:MED14-independent group 3 enhancer GRCh37_chrX:41944854-41946053 [Gene]
LOC126863242:MED14-independent group 3 enhancer GRCh37_chrX:42835354-42836553 [Gene]
LOC126863243:MED14-independent group 3 enhancer GRCh37_chrX:43035494-43036693 [Gene]
LOC129391298:MPRA-validated peak7375 silencer [Gene]
LOC129391299:MPRA-validated peak7376 silencer [Gene]
NDP-AS1:NDP antisense RNA 1 [Gene - HGNC]
PPP1R2C:PPP1R2C family member C [Gene - OMIM - HGNC]
LOC125467738:Sharpr-MPRA regulatory region 14962 [Gene]
LOC113875026:Sharpr-MPRA regulatory region 2101 [Gene]
CASK:calcium/calmodulin dependent serine protein kinase [Gene - OMIM - HGNC]
MAOA:monoamine oxidase A [Gene - OMIM - HGNC]
MAOB:monoamine oxidase B [Gene - OMIM - HGNC]
NDP:norrin cystine knot growth factor NDP [Gene - OMIM - HGNC]
PINCR:p53-induced noncoding RNA [Gene - HGNC]

Variant type:

copy number loss

Cytogenetic location:

Xp11.4-11.3

Genomic location:

Preferred name:

GRCh38/hg38 Xp11.4-11.3(chrX:41823849-44240337)x1

HGVS:

NC_000023.11:g.(?_41823849)_(44240337_?)del
NC_000023.10:g.(?_41683102)_(44099583_?)del
NC_000023.9:g.(?_41568046)_(43984527_?)del

Links:

dbVar: nssv578437; dbVar: nsv531782

Observations:

Condition(s)

Name:: See cases [See the Variation display for details]
Identifiers:

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364581[uid] (1)
Taxonomy
Diapriidae sp. 10BBCHY-2057 cytochrome oxidase subunit 1 (COI) gene, partial cds...
Diapriidae sp. 10BBCHY-2057 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
gi|1503021093|gnl|uoguelph|BBHYK099 OI-5P|gb|MG485116.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000080447	GeneDx	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	de novo	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

SCV000080447

GeneDx

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))

Pathogenic
(Aug 12, 2011)

de novo

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	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, et al.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

PubMed [citation]

PMID:: 21844811
PMCID:: PMC3661946

Details of each submission

From GeneDx, SCV000080447.5

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: Oct 14, 2023

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