GRCh38/hg38 1q21.1-21.2(chr1:146987841-148436984)x1 AND See cases

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 12, 2011
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000148176.4

Allele description [Variation Report for GRCh38/hg38 1q21.1-21.2(chr1:146987841-148436984)x1]

GRCh38/hg38 1q21.1-21.2(chr1:146987841-148436984)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]
RNVU1-1:RNA, variant U1 small nuclear 1 [Gene - HGNC]
RNVU1-3:RNA, variant U1 small nuclear 3 [Gene - HGNC]
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]
LINC01138:long intergenic non-protein coding RNA 1138 [Gene - 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]
MIR6077:microRNA 6077 [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(chr1:146987841-148436984)x1

HGVS:

NC_000001.11:g.(?_146987841)_(148436984_?)del
NC_000001.10:g.(?_145425395)_(147909094_?)del
NC_000001.9:g.(?_144136752)_(146375718_?)del

Note:

N.B.: Remap data for this variant included multiple placements, suggesting it falls within a region of the genome that significantly changed between assemblies. We present the highest-scoring remap placement here; however the variant's location should be interpreted with caution.

Links:

dbVar: nssv579606; dbVar: nssv579614; dbVar: nsv1067590

Observations:

Condition(s)

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

Recent activity

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3-ketoacyl-ACP reductase [Sorangium cellulosum]
3-ketoacyl-ACP reductase [Sorangium cellulosum]
gi|1566495796|gnl|PRJNA297370|SOCEG 06190|gb|AUX20155.1|

Protein
hypothetical protein BN424_3115 [Carnobacterium maltaromaticum LMA28]
hypothetical protein BN424_3115 [Carnobacterium maltaromaticum LMA28]
gi|508081379|emb|CCO12536.2|

Protein
LOC125316809 [Homo sapiens]
LOC125316809 [Homo sapiens]
Gene ID:125316809

Gene
LOC127888308 [Homo sapiens]
LOC127888308 [Homo sapiens]
Gene ID:127888308

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000190754	ISCA site 17 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000190755	ISCA site 4 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	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

SCV000190754

ISCA site 17

See additional submitters

criteria provided, single submitter

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

Pathogenic
(Aug 12, 2011)

unknown

clinical testing

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

SCV000190755

ISCA site 4

See additional submitters

criteria provided, single submitter

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

Pathogenic
(Aug 12, 2011)

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	not provided	yes	2	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 17, SCV000190754.3

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

From ISCA site 4, SCV000190755.3

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

Last Updated: May 7, 2024

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