GRCh38/hg38 2q13-14.1(chr2:110631042-112354279)x1 AND See cases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 18, 2014
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:: RCV000142199.7

Allele description [Variation Report for GRCh38/hg38 2q13-14.1(chr2:110631042-112354279)x1]

GRCh38/hg38 2q13-14.1(chr2:110631042-112354279)x1

Genes:

ACOXL-AS1:ACOXL antisense RNA 1 [Gene - HGNC]
LOC129934557:ATAC-STARR-seq lymphoblastoid active region 16371 [Gene]
LOC129934558:ATAC-STARR-seq lymphoblastoid active region 16374 [Gene]
LOC129934559:ATAC-STARR-seq lymphoblastoid active region 16375 [Gene]
LOC129934560:ATAC-STARR-seq lymphoblastoid active region 16376 [Gene]
LOC129934561:ATAC-STARR-seq lymphoblastoid active region 16377 [Gene]
LOC129934562:ATAC-STARR-seq lymphoblastoid active region 16378 [Gene]
LOC129934563:ATAC-STARR-seq lymphoblastoid active region 16379 [Gene]
LOC129934564:ATAC-STARR-seq lymphoblastoid active region 16380 [Gene]
LOC129934565:ATAC-STARR-seq lymphoblastoid active region 16381 [Gene]
LOC129934568:ATAC-STARR-seq lymphoblastoid active region 16383 [Gene]
LOC129934569:ATAC-STARR-seq lymphoblastoid active region 16384 [Gene]
LOC129934571:ATAC-STARR-seq lymphoblastoid active region 16385 [Gene]
LOC129934572:ATAC-STARR-seq lymphoblastoid active region 16386 [Gene]
LOC129934573:ATAC-STARR-seq lymphoblastoid active region 16387 [Gene]
LOC129934576:ATAC-STARR-seq lymphoblastoid active region 16388 [Gene]
LOC129934577:ATAC-STARR-seq lymphoblastoid active region 16389 [Gene]
LOC129934578:ATAC-STARR-seq lymphoblastoid active region 16390 [Gene]
LOC129934566:ATAC-STARR-seq lymphoblastoid silent region 11865 [Gene]
LOC129934567:ATAC-STARR-seq lymphoblastoid silent region 11866 [Gene]
LOC129934570:ATAC-STARR-seq lymphoblastoid silent region 11867 [Gene]
LOC129934574:ATAC-STARR-seq lymphoblastoid silent region 11868 [Gene]
LOC129934575:ATAC-STARR-seq lymphoblastoid silent region 11869 [Gene]
LOC129934579:ATAC-STARR-seq lymphoblastoid silent region 11870 [Gene]
LOC129934580:ATAC-STARR-seq lymphoblastoid silent region 11871 [Gene]
BCL2L11:BCL2 like 11 [Gene - OMIM - HGNC]
BUB1:BUB1 mitotic checkpoint serine/threonine kinase [Gene - OMIM - HGNC]
LOC126806307:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:111556532-111557731 [Gene]
LOC115945185:CRISPRi-validated cis-regulatory element chr2.4107 [Gene]
MERTK:MER proto-oncogene, tyrosine kinase [Gene - OMIM - HGNC]
MIR4435-2HG:MIR4435-2 host gene [Gene - OMIM - HGNC]
LOC129388900:MPRA-validated peak3818 silencer [Gene]
LOC122817726:OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:112462827-112463612 and GRCh37_chr2:112463613-112464396 [Gene]
LOC126806308:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:111789964-111791163 [Gene]
LOC126806309:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:112252044-112253243 [Gene]
LOC122817727:Sharpr-MPRA regulatory region 10261 [Gene]
LOC122817723:Sharpr-MPRA regulatory region 12654 [Gene]
LOC112806037:Sharpr-MPRA regulatory region 3720 [Gene]
LOC122817725:Sharpr-MPRA regulatory region 6991 [Gene]
LOC120961779:Sharpr-MPRA regulatory region 7769 [Gene]
LOC122817724:Sharpr-MPRA regulatory region 8028 [Gene]
ACOXL:acyl-CoA oxidase like [Gene - HGNC]
ANAPC1:anaphase promoting complex subunit 1 [Gene - OMIM - HGNC]
FBLN7:fibulin 7 [Gene - OMIM - HGNC]
MIR4435-2:microRNA 4435-2 [Gene - HGNC]
MIR4771-2:microRNA 4771-2 [Gene - HGNC]
SOCAR:serous ovarian cancer associated RNA [Gene - HGNC]
SNORD132:small nucleolar RNA, C/D box 132 [Gene - HGNC]
TMEM87B:transmembrane protein 87B [Gene - OMIM - HGNC]
LOC105373559:uncharacterized LOC105373559 [Gene]
ZC3H6:zinc finger CCCH-type containing 6 [Gene - HGNC]
ZC3H8:zinc finger CCCH-type containing 8 [Gene - HGNC]

Variant type:

copy number loss

Cytogenetic location:

2q13-14.1

Genomic location:

Preferred name:

GRCh38/hg38 2q13-14.1(chr2:110631042-112354279)x1

HGVS:

NC_000002.12:g.(?_110631042)_(112354279_?)del
NC_000002.10:g.(?_111105088)_(112828327_?)del
NC_000002.11:g.(?_111388619)_(113111856_?)del

Links:

dbVar: nssv3397415; dbVar: nsv996026

Observations:

Condition(s)

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

Recent activity

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hypothetical protein F2P81_004602 [Scophthalmus maximus]
hypothetical protein F2P81_004602 [Scophthalmus maximus]
gi|1786652150|gb|KAF0043265.1||gnl| EVO|cds.evm.model.Lg04.594

Protein
Mus musculus tumor protein D52-like 1 (Tpd52l1), transcript variant 4, mRNA
Mus musculus tumor protein D52-like 1 (Tpd52l1), transcript variant 4, mRNA
gi|2707155993|ref|NM_001359366.2|

Nucleotide
PREDICTED: Danio rerio cytochrome P450, family 2, subfamily R, polypeptide 1 (cy...
PREDICTED: Danio rerio cytochrome P450, family 2, subfamily R, polypeptide 1 (cyp2r1), transcript variant X2, mRNA
gi|2800593577|ref|XM_068222335.1|

Nucleotide
GINS complex subunit 2 [Danio rerio]
GINS complex subunit 2 [Danio rerio]
gi|66267503|gb|AAH95711.1|

Protein
kynurenine--oxoglutarate transaminase 1 isoform X2 [Mus musculus]
kynurenine--oxoglutarate transaminase 1 isoform X2 [Mus musculus]
gi|568914268|ref|XP_006498380.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000183455	ISCA site 1 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Uncertain significance (Jul 18, 2014)	paternal	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

SCV000183455

ISCA site 1

See additional submitters

no assertion criteria provided

Uncertain significance
(Jul 18, 2014)

paternal

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	paternal	yes	1	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, SCV000183455.4

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

Last Updated: May 7, 2024

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