GRCh38/hg38 1q21.1-21.2(chr1:146987841-148355961)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 9, 2013
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000142798.5

Allele description [Variation Report for GRCh38/hg38 1q21.1-21.2(chr1:146987841-148355961)x1]

GRCh38/hg38 1q21.1-21.2(chr1:146987841-148355961)x1

Genes:

LOC129931358:ATAC-STARR-seq lymphoblastoid active region 1635 [Gene]
LOC129931359:ATAC-STARR-seq lymphoblastoid active region 1637 [Gene]
LOC129931360:ATAC-STARR-seq lymphoblastoid active region 1638 [Gene]
LOC129931361:ATAC-STARR-seq lymphoblastoid active region 1639 [Gene]
LOC129931362:ATAC-STARR-seq lymphoblastoid active region 1640 [Gene]
LOC129931363:ATAC-STARR-seq lymphoblastoid active region 1641 [Gene]
LOC129931352:ATAC-STARR-seq lymphoblastoid silent region 1277 [Gene]
LOC129931353:ATAC-STARR-seq lymphoblastoid silent region 1278 [Gene]
LOC129931354:ATAC-STARR-seq lymphoblastoid silent region 1279 [Gene]
LOC129931355:ATAC-STARR-seq lymphoblastoid silent region 1280 [Gene]
LOC129931356:ATAC-STARR-seq lymphoblastoid silent region 1281 [Gene]
LOC129931357:ATAC-STARR-seq lymphoblastoid silent region 1282 [Gene]
BCL9:BCL9 transcription coactivator [Gene - OMIM - HGNC]
LOC126805854:BRD4-independent group 4 enhancer GRCh37_chr1:146764440-146765639 [Gene]
LOC126805852:CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:146501494-146502693 [Gene]
GPR89B:G protein-coupled receptor 89B [Gene - OMIM - HGNC]
LOC111556113:HNF4 motif-containing MPRA enhancer 9 [Gene]
LOC129388602:MPRA-validated peak400 silencer [Gene]
LOC129388603:MPRA-validated peak402 silencer [Gene]
LOC129388604:MPRA-validated peak403 silencer [Gene]
NBPF11:NBPF member 11 [Gene - OMIM - HGNC]
NBPF12:NBPF member 12 [Gene - OMIM - HGNC]
LOC126805853:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:146633127-146634326 [Gene]
RNVU1-7:RNA, variant U1 small nuclear 7 [Gene - HGNC]
RNVU1-8:RNA, variant U1 small nuclear 8 [Gene - HGNC]
LOC121725052:Sharpr-MPRA regulatory region 10305 [Gene]
LOC122128420:Sharpr-MPRA regulatory region 3144 [Gene]
LOC112577490:Sharpr-MPRA regulatory region 3868 [Gene]
LOC121725051:Sharpr-MPRA regulatory region 5908 [Gene]
LOC121725053:Sharpr-MPRA regulatory region 879 [Gene]
LOC110121261:VISTA enhancer hs2126 [Gene]
ACP6:acid phosphatase 6, lysophosphatidic [Gene - OMIM - HGNC]
CHD1L:chromodomain helicase DNA binding protein 1 like [Gene - OMIM - HGNC]
FMO5:flavin containing dimethylaniline monoxygenase 5 [Gene - OMIM - HGNC]
GJA5:gap junction protein alpha 5 [Gene - OMIM - HGNC]
GJA8:gap junction protein alpha 8 [Gene - OMIM - HGNC]
LINC01731:long intergenic non-protein coding RNA 1731 [Gene - HGNC]
LINC02805:long intergenic non-protein coding RNA 2805 [Gene - HGNC]
LINC02806:long intergenic non-protein coding RNA 2806 [Gene - HGNC]
LINC00624:long intergenic non-protein coding RNA 624 [Gene - HGNC]
MIR5087:microRNA 5087 [Gene - HGNC]
PRKAB2:protein kinase AMP-activated non-catalytic subunit beta 2 [Gene - OMIM - HGNC]
TRN-GTT9-2:tRNA-Asn (anticodon GTT) 9-2 [Gene - HGNC]
TRQ-CTG3-2:tRNA-Gln (anticodon CTG) 3-2 [Gene - HGNC]
TRQ-CTG4-1:tRNA-Gln (anticodon CTG) 4-1 [Gene - HGNC]
TRQ-CTG7-1:tRNA-Gln (anticodon CTG) 7-1 [Gene - HGNC]
TRH-GTG1-2:tRNA-His (anticodon GTG) 1-2 [Gene - HGNC]
TRH-GTG1-3:tRNA-His (anticodon GTG) 1-3 [Gene - HGNC]
TRH-GTG1-4:tRNA-His (anticodon GTG) 1-4 [Gene - HGNC]
LOC101927468:uncharacterized LOC101927468 [Gene]
LOC128071544:uncharacterized LOC128071544 [Gene]

Variant type:

copy number loss

Cytogenetic location:

1q21.1-21.2

Genomic location:

Preferred name:

GRCh38/hg38 1q21.1-21.2(chr1:146987841-148355961)x1

HGVS:

NC_000001.11:g.(?_146987841)_(148355961_?)del
NC_000001.10:g.(?_145626237)_(147828089_?)del
NC_000001.9:g.(?_144337594)_(146294713_?)del

Links:

dbVar: nssv1494838; dbVar: nssv1601722; dbVar: nssv1602013; dbVar: nssv1604154; dbVar: nssv1604370; dbVar: nssv1604655; dbVar: nssv1608112; dbVar: nssv1609367; dbVar: nssv1609603; dbVar: nssv1610085; dbVar: nsv869300

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
SCV000178365	ISCA site 1 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Pathogenic (Jan 9, 2013)	maternal, paternal, unknown	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

SCV000178365

ISCA site 1

See additional submitters

no assertion criteria provided

Pathogenic
(Jan 9, 2013)

maternal, paternal, unknown

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	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	yes	5	not provided	not provided	not provided	not provided	clinical testing
not provided	paternal	yes	2	not provided	not provided	not provided	not provided	clinical testing
human	not provided	yes	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]

PMID:: 20466091
PMCID:: PMC2869000

Details of each submission

From ISCA site 1, SCV000178365.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)
2	not provided	1	not provided	not provided	clinical testing	PubMed (1)
3	not provided	1	not provided	not provided	clinical testing	PubMed (1)
4	not provided	1	not provided	not provided	clinical testing	PubMed (1)
5	not provided	1	not provided	not provided	clinical testing	PubMed (1)
6	not provided	1	not provided	not provided	clinical testing	PubMed (1)
7	not provided	1	not provided	not provided	clinical testing	PubMed (1)
8	not provided	1	not provided	not provided	clinical testing	PubMed (1)
9	human	1	not provided	not provided	clinical testing	PubMed (1)
10	human	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	maternal	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
2	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
3	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
4	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
5	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
6	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
7	paternal	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
8	paternal	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
9	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
10	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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