GRCh38/hg38 1q21.3(chr1:153759563-154219803)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:: RCV000053883.4

Allele description [Variation Report for GRCh38/hg38 1q21.3(chr1:153759563-154219803)x1]

GRCh38/hg38 1q21.3(chr1:153759563-154219803)x1

Genes:

LOC129931486:ATAC-STARR-seq lymphoblastoid active region 1755 [Gene]
LOC129931487:ATAC-STARR-seq lymphoblastoid active region 1756 [Gene]
LOC129931488:ATAC-STARR-seq lymphoblastoid active region 1757 [Gene]
LOC129931489:ATAC-STARR-seq lymphoblastoid active region 1758 [Gene]
LOC129931490:ATAC-STARR-seq lymphoblastoid active region 1759 [Gene]
LOC129931491:ATAC-STARR-seq lymphoblastoid active region 1760 [Gene]
LOC129931492:ATAC-STARR-seq lymphoblastoid active region 1761 [Gene]
LOC129931494:ATAC-STARR-seq lymphoblastoid active region 1762 [Gene]
LOC129931495:ATAC-STARR-seq lymphoblastoid active region 1770 [Gene]
LOC129931496:ATAC-STARR-seq lymphoblastoid active region 1771 [Gene]
LOC129931497:ATAC-STARR-seq lymphoblastoid active region 1773 [Gene]
LOC129931485:ATAC-STARR-seq lymphoblastoid silent region 1345 [Gene]
LOC129931493:ATAC-STARR-seq lymphoblastoid silent region 1347 [Gene]
LOC126805871:BRD4-independent group 4 enhancer GRCh37_chr1:153935601-153936800 [Gene]
LOC126805872:BRD4-independent group 4 enhancer GRCh37_chr1:153962963-153964162 [Gene]
CRTC2:CREB regulated transcription coactivator 2 [Gene - OMIM - HGNC]
DENND4B:DENN domain containing 4B [Gene - OMIM - HGNC]
GATAD2B:GATA zinc finger domain containing 2B [Gene - OMIM - HGNC]
JTB-DT:JTB divergent transcript [Gene - HGNC]
RAB13:RAB13, member RAS oncogene family [Gene - OMIM - HGNC]
LOC122128433:Sharpr-MPRA regulatory region 11874 [Gene]
LOC122128430:Sharpr-MPRA regulatory region 14566 [Gene]
LOC122128431:Sharpr-MPRA regulatory region 2699 [Gene]
LOC122128432:Sharpr-MPRA regulatory region 4321 [Gene]
CREB3L4:cAMP responsive element binding protein 3 like 4 [Gene - OMIM - HGNC]
C1orf43:chromosome 1 open reading frame 43 [Gene - OMIM - HGNC]
CFAP141:cilia and flagella associated protein 141 [Gene - HGNC]
INTS3:integrator complex subunit 3 [Gene - OMIM - HGNC]
JTB:jumping translocation breakpoint [Gene - OMIM - HGNC]
MIR190B:microRNA 190b [Gene - HGNC]
MIR5698:microRNA 5698 [Gene - HGNC]
MIR6737:microRNA 6737 [Gene - HGNC]
NUP210L:nucleoporin 210 like [Gene - HGNC]
RPS27:ribosomal protein S27 [Gene - OMIM - HGNC]
SLC27A3:solute carrier family 27 member 3 [Gene - OMIM - HGNC]
SLC39A1:solute carrier family 39 member 1 [Gene - OMIM - HGNC]
TPM3:tropomyosin 3 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

GRCh38/hg38 1q21.3(chr1:153759563-154219803)x1

HGVS:

NC_000001.11:g.(?_153759563)_(154219803_?)del
NC_000001.10:g.(?_153732039)_(154192279_?)del
NC_000001.9:g.(?_151998663)_(152458903_?)del

Links:

dbVar: nssv577222; dbVar: nsv532551

Observations:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000081246	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

SCV000081246

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, SCV000081246.4

#	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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