GRCh38/hg38 1q43(chr1:239631841-242609012)x3 AND See cases

Germline classification:: Uncertain significance (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:: RCV000051587.5

Allele description [Variation Report for GRCh38/hg38 1q43(chr1:239631841-242609012)x3]

GRCh38/hg38 1q43(chr1:239631841-242609012)x3

Genes:

LOC129932889:ATAC-STARR-seq lymphoblastoid active region 2828 [Gene]
LOC129932890:ATAC-STARR-seq lymphoblastoid active region 2829 [Gene]
LOC129932891:ATAC-STARR-seq lymphoblastoid active region 2830 [Gene]
LOC129932887:ATAC-STARR-seq lymphoblastoid silent region 2006 [Gene]
LOC129932888:ATAC-STARR-seq lymphoblastoid silent region 2007 [Gene]
LOC126806071:BRD4-independent group 4 enhancer GRCh37_chr1:242611784-242612983 [Gene]
LOC126806069:CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:240421073-240422272 [Gene]
CHML:CHM like Rab escort protein [Gene - OMIM - HGNC]
CHRM3-AS1:CHRM3 antisense RNA 1 [Gene - HGNC]
CHRM3-AS2:CHRM3 antisense RNA 2 [Gene - HGNC]
LOC115804253:CRISPRi-validated cis-regulatory element chr1.12743 [Gene]
LOC126806070:MED14-independent group 3 enhancer GRCh37_chr1:241099640-241100839 [Gene]
LOC129388792:MPRA-validated peak794 silencer [Gene]
LOC129388793:MPRA-validated peak795 silencer [Gene]
LOC129388794:MPRA-validated peak797 silencer [Gene]
LOC129388795:MPRA-validated peak799 silencer [Gene]
LOC129388796:MPRA-validated peak800 silencer [Gene]
LOC129388797:MPRA-validated peak801 silencer [Gene]
LOC129388798:MPRA-validated peak802 silencer [Gene]
LOC132088685:Neanderthal introgressed variant-containing enhancer experimental_6389 [Gene]
LOC132088686:Neanderthal introgressed variant-containing enhancer experimental_6394 [Gene]
LOC112577565:Sharpr-MPRA regulatory region 3307 [Gene]
LOC122152349:Sharpr-MPRA regulatory region 3663 [Gene]
WDR64:WD repeat domain 64 [Gene - HGNC]
BECN2:beclin 2 [Gene - OMIM - HGNC]
CHRM3:cholinergic receptor muscarinic 3 [Gene - OMIM - HGNC]
EXO1:exonuclease 1 [Gene - OMIM - HGNC]
FMN2:formin 2 [Gene - OMIM - HGNC]
FH:fumarate hydratase [Gene - OMIM - HGNC]
GREM2:gremlin 2, DAN family BMP antagonist [Gene - OMIM - HGNC]
KMO:kynurenine 3-monooxygenase [Gene - OMIM - HGNC]
MIR3123:microRNA 3123 [Gene - HGNC]
MAP1LC3C:microtubule associated protein 1 light chain 3 gamma [Gene - OMIM - HGNC]
OPN3:opsin 3 [Gene - OMIM - HGNC]
PLD5:phospholipase D family member 5 [Gene - HGNC]
RGS7:regulator of G protein signaling 7 [Gene - OMIM - HGNC]
LOC100506929:uncharacterized LOC100506929 [Gene]

Variant type:

copy number gain

Cytogenetic location:

1q43

Genomic location:

Preferred name:

GRCh38/hg38 1q43(chr1:239631841-242609012)x3

HGVS:

NC_000001.11:g.(?_239631841)_(242609012_?)dup
NC_000001.10:g.(?_239795141)_(242772314_?)dup
NC_000001.9:g.(?_237861764)_(240838937_?)dup

Links:

dbVar: nssv580729; dbVar: nsv530110

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
SCV000078935	ISCA site 15 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Uncertain significance (Aug 12, 2011)	not provided	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

SCV000078935

ISCA site 15

See additional submitters

criteria provided, single submitter

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

Uncertain significance
(Aug 12, 2011)

not provided

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	not provided	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 ISCA site 15, SCV000078935.4

#	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	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: Oct 14, 2023

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