GRCh38/hg38 7p21.2-21.1(chr7:15133711-19642829)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:: RCV000052289.5

Allele description [Variation Report for GRCh38/hg38 7p21.2-21.1(chr7:15133711-19642829)x1]

GRCh38/hg38 7p21.2-21.1(chr7:15133711-19642829)x1

Genes:

LOC129998006:ATAC-STARR-seq lymphoblastoid active region 25669 [Gene]
LOC129998007:ATAC-STARR-seq lymphoblastoid active region 25670 [Gene]
LOC129998008:ATAC-STARR-seq lymphoblastoid active region 25671 [Gene]
LOC129998009:ATAC-STARR-seq lymphoblastoid active region 25672 [Gene]
LOC129998014:ATAC-STARR-seq lymphoblastoid active region 25675 [Gene]
LOC129998015:ATAC-STARR-seq lymphoblastoid active region 25676 [Gene]
LOC129998016:ATAC-STARR-seq lymphoblastoid active region 25677 [Gene]
LOC129998017:ATAC-STARR-seq lymphoblastoid active region 25678 [Gene]
LOC129998018:ATAC-STARR-seq lymphoblastoid active region 25679 [Gene]
LOC129998019:ATAC-STARR-seq lymphoblastoid active region 25680 [Gene]
LOC129998021:ATAC-STARR-seq lymphoblastoid active region 25682 [Gene]
LOC129998004:ATAC-STARR-seq lymphoblastoid silent region 17981 [Gene]
LOC129998005:ATAC-STARR-seq lymphoblastoid silent region 17982 [Gene]
LOC129998010:ATAC-STARR-seq lymphoblastoid silent region 17983 [Gene]
LOC129998011:ATAC-STARR-seq lymphoblastoid silent region 17984 [Gene]
LOC129998012:ATAC-STARR-seq lymphoblastoid silent region 17985 [Gene]
LOC129998013:ATAC-STARR-seq lymphoblastoid silent region 17986 [Gene]
LOC129998020:ATAC-STARR-seq lymphoblastoid silent region 17987 [Gene]
LOC126859949:BRD4-independent group 4 enhancer GRCh37_chr7:16116228-16117427 [Gene]
LOC126859955:BRD4-independent group 4 enhancer GRCh37_chr7:19183777-19184976 [Gene]
CRPPA:CDP-L-ribitol pyrophosphorylase A [Gene - OMIM - HGNC]
CRPPA-AS1:CRPPA antisense RNA 1 [Gene - HGNC]
FERD3L:Fer3 like bHLH transcription factor [Gene - OMIM - HGNC]
LOC111591502:GATA motif-containing MPRA enhancer 275 [Gene]
HDAC9-AS1:HDAC9 antisense RNA 1 [Gene - HGNC]
LOC126859951:MED14-independent group 3 enhancer GRCh37_chr7:17411084-17412283 [Gene]
LOC126859953:MED14-independent group 3 enhancer GRCh37_chr7:18459909-18461108 [Gene]
LOC129389757:MPRA-validated peak6410 silencer [Gene]
LOC129389758:MPRA-validated peak6411 silencer [Gene]
LOC129389759:MPRA-validated peak6414 silencer [Gene]
LOC129389760:MPRA-validated peak6415 silencer [Gene]
LOC129389761:MPRA-validated peak6419 silencer [Gene]
LOC129389762:MPRA-validated peak6420 silencer [Gene]
LOC132089521:Neanderthal introgressed variant-containing enhancer experimental_98149 [Gene]
LOC126859950:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:17273731-17274930 [Gene]
LOC126859952:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:17445039-17446238 [Gene]
LOC126859954:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:18548259-18549458 [Gene]
LOC123924911:Sharpr-MPRA regulatory region 11479 [Gene]
LOC123924910:Sharpr-MPRA regulatory region 12164 [Gene]
LOC113687203:Sharpr-MPRA regulatory region 14752 [Gene]
LOC123924908:Sharpr-MPRA regulatory region 14985 [Gene]
LOC123924915:Sharpr-MPRA regulatory region 1729 [Gene]
LOC123924909:Sharpr-MPRA regulatory region 6485 [Gene]
LOC123924914:Sharpr-MPRA regulatory region 6645 [Gene]
LOC123924913:Sharpr-MPRA regulatory region 7324 [Gene]
LOC123924912:Sharpr-MPRA regulatory regions 10536 and 6796 [Gene]
LOC110120728:VISTA enhancer hs644 [Gene]
AGMO:alkylglycerol monooxygenase [Gene - OMIM - HGNC]
ANKMY2:ankyrin repeat and MYND domain containing 2 [Gene - HGNC]
AGR2:anterior gradient 2, protein disulphide isomerase family member [Gene - OMIM - HGNC]
AGR3:anterior gradient 3, protein disulphide isomerase family member [Gene - OMIM - HGNC]
AHR:aryl hydrocarbon receptor [Gene - OMIM - HGNC]
BZW2:basic leucine zipper and W2 domains 2 [Gene - OMIM - HGNC]
LOC110121290:eExon 18 TWIST1 limb enhancer [Gene]
LOC110121291:eExon 19 TWIST1 limb enhancer [Gene]
HDAC9:histone deacetylase 9 [Gene - OMIM - HGNC]
LRRC72:leucine rich repeat containing 72 [Gene - HGNC]
LINC02587:long intergenic non-protein coding RNA 2587 [Gene - HGNC]
LINC02888:long intergenic non-protein coding RNA 2888 [Gene - HGNC]
LINC02889:long intergenic non-protein coding RNA 2889 [Gene - HGNC]
LOC128772304:melanoma risk locus-associated MPRA allelic enhancer 7:17134708 [Gene]
MEOX2:mesenchyme homeobox 2 [Gene - OMIM - HGNC]
MIR1302-6:microRNA 1302-6 [Gene - HGNC]
PRPS1L1:phosphoribosyl pyrophosphate synthetase 1 like 1 [Gene - OMIM - HGNC]
SOSTDC1:sclerostin domain containing 1 [Gene - OMIM - HGNC]
SNX13:sorting nexin 13 [Gene - OMIM - HGNC]
TSPAN13:tetraspanin 13 [Gene - OMIM - HGNC]
TWIST1:twist family bHLH transcription factor 1 [Gene - OMIM - HGNC]
LOC105375166:uncharacterized LOC105375166 [Gene]

Variant type:

copy number loss

Cytogenetic location:

7p21.2-21.1

Genomic location:

Preferred name:

GRCh38/hg38 7p21.2-21.1(chr7:15133711-19642829)x1

HGVS:

NC_000007.14:g.(?_15133711)_(19642829_?)del
NC_000007.12:g.(?_15139861)_(19648977_?)del
NC_000007.13:g.(?_15173336)_(19682452_?)del

Links:

dbVar: nssv578178; dbVar: nsv530994

Observations:

Condition(s)

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

Recent activity

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Model organism or animal sample from Myrmotherula axillaris
Model organism or animal sample from Myrmotherula axillaris

biosample
oxysterol-binding protein-related protein 1 isoform 3 [Homo sapiens]
oxysterol-binding protein-related protein 1 isoform 3 [Homo sapiens]
gi|335353788|ref|NP_001229437.1|

Protein
AMSG_12409 [Thecamonas trahens ATCC 50062]
AMSG_12409 [Thecamonas trahens ATCC 50062]
Gene ID:25570323

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000079640	ISCA site 14 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

SCV000079640

ISCA site 14

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	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 14, SCV000079640.4

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

Last Updated: May 7, 2024

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