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GRCh38/hg38 2q11.2(chr2:98411773-101636907)x1 AND See cases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 7, 2011
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:
RCV000139206.5

Allele description [Variation Report for GRCh38/hg38 2q11.2(chr2:98411773-101636907)x1]

GRCh38/hg38 2q11.2(chr2:98411773-101636907)x1

Genes:
  • AFF3:ALF transcription elongation factor 3 [Gene - OMIM - HGNC]
  • LOC129934405:ATAC-STARR-seq lymphoblastoid active region 16257 [Gene]
  • LOC129934406:ATAC-STARR-seq lymphoblastoid active region 16258 [Gene]
  • LOC129934408:ATAC-STARR-seq lymphoblastoid active region 16259 [Gene]
  • LOC129934409:ATAC-STARR-seq lymphoblastoid active region 16260 [Gene]
  • LOC129934410:ATAC-STARR-seq lymphoblastoid active region 16261 [Gene]
  • LOC129934411:ATAC-STARR-seq lymphoblastoid active region 16262 [Gene]
  • LOC129934412:ATAC-STARR-seq lymphoblastoid active region 16263 [Gene]
  • LOC129934414:ATAC-STARR-seq lymphoblastoid active region 16264 [Gene]
  • LOC129934415:ATAC-STARR-seq lymphoblastoid active region 16265 [Gene]
  • LOC129934416:ATAC-STARR-seq lymphoblastoid active region 16266 [Gene]
  • LOC129934417:ATAC-STARR-seq lymphoblastoid active region 16267 [Gene]
  • LOC129934418:ATAC-STARR-seq lymphoblastoid active region 16268 [Gene]
  • LOC129934419:ATAC-STARR-seq lymphoblastoid active region 16269 [Gene]
  • LOC129934423:ATAC-STARR-seq lymphoblastoid active region 16270 [Gene]
  • LOC129934424:ATAC-STARR-seq lymphoblastoid active region 16271 [Gene]
  • LOC129934427:ATAC-STARR-seq lymphoblastoid active region 16276 [Gene]
  • LOC129934428:ATAC-STARR-seq lymphoblastoid active region 16277 [Gene]
  • LOC129934429:ATAC-STARR-seq lymphoblastoid active region 16278 [Gene]
  • LOC129934430:ATAC-STARR-seq lymphoblastoid active region 16279 [Gene]
  • LOC129934431:ATAC-STARR-seq lymphoblastoid active region 16280 [Gene]
  • LOC129934432:ATAC-STARR-seq lymphoblastoid active region 16281 [Gene]
  • LOC129934433:ATAC-STARR-seq lymphoblastoid active region 16284 [Gene]
  • LOC129934434:ATAC-STARR-seq lymphoblastoid active region 16285 [Gene]
  • LOC129934435:ATAC-STARR-seq lymphoblastoid active region 16286 [Gene]
  • LOC129934438:ATAC-STARR-seq lymphoblastoid active region 16288 [Gene]
  • LOC129934441:ATAC-STARR-seq lymphoblastoid active region 16289 [Gene]
  • LOC129934442:ATAC-STARR-seq lymphoblastoid active region 16290 [Gene]
  • LOC129934444:ATAC-STARR-seq lymphoblastoid active region 16291 [Gene]
  • LOC129934445:ATAC-STARR-seq lymphoblastoid active region 16292 [Gene]
  • LOC129934446:ATAC-STARR-seq lymphoblastoid active region 16293 [Gene]
  • LOC129934447:ATAC-STARR-seq lymphoblastoid active region 16294 [Gene]
  • LOC129934451:ATAC-STARR-seq lymphoblastoid active region 16295 [Gene]
  • LOC129934452:ATAC-STARR-seq lymphoblastoid active region 16296 [Gene]
  • LOC129934453:ATAC-STARR-seq lymphoblastoid active region 16297 [Gene]
  • LOC129934454:ATAC-STARR-seq lymphoblastoid active region 16298 [Gene]
  • LOC129934457:ATAC-STARR-seq lymphoblastoid active region 16299 [Gene]
  • LOC129934459:ATAC-STARR-seq lymphoblastoid active region 16300 [Gene]
  • LOC129934460:ATAC-STARR-seq lymphoblastoid active region 16301 [Gene]
  • LOC129934465:ATAC-STARR-seq lymphoblastoid active region 16302 [Gene]
  • LOC129934407:ATAC-STARR-seq lymphoblastoid silent region 11800 [Gene]
  • LOC129934413:ATAC-STARR-seq lymphoblastoid silent region 11801 [Gene]
  • LOC129934420:ATAC-STARR-seq lymphoblastoid silent region 11802 [Gene]
  • LOC129934421:ATAC-STARR-seq lymphoblastoid silent region 11803 [Gene]
  • LOC129934422:ATAC-STARR-seq lymphoblastoid silent region 11804 [Gene]
  • LOC129934425:ATAC-STARR-seq lymphoblastoid silent region 11805 [Gene]
  • LOC129934426:ATAC-STARR-seq lymphoblastoid silent region 11806 [Gene]
  • LOC129934436:ATAC-STARR-seq lymphoblastoid silent region 11808 [Gene]
  • LOC129934437:ATAC-STARR-seq lymphoblastoid silent region 11809 [Gene]
  • LOC129934439:ATAC-STARR-seq lymphoblastoid silent region 11810 [Gene]
  • LOC129934440:ATAC-STARR-seq lymphoblastoid silent region 11811 [Gene]
  • LOC129934443:ATAC-STARR-seq lymphoblastoid silent region 11813 [Gene]
  • LOC129934448:ATAC-STARR-seq lymphoblastoid silent region 11814 [Gene]
  • LOC129934449:ATAC-STARR-seq lymphoblastoid silent region 11815 [Gene]
  • LOC129934450:ATAC-STARR-seq lymphoblastoid silent region 11816 [Gene]
  • LOC129934455:ATAC-STARR-seq lymphoblastoid silent region 11818 [Gene]
  • LOC129934456:ATAC-STARR-seq lymphoblastoid silent region 11819 [Gene]
  • LOC129934458:ATAC-STARR-seq lymphoblastoid silent region 11820 [Gene]
  • LOC129934461:ATAC-STARR-seq lymphoblastoid silent region 11823 [Gene]
  • LOC129934462:ATAC-STARR-seq lymphoblastoid silent region 11824 [Gene]
  • LOC129934463:ATAC-STARR-seq lymphoblastoid silent region 11825 [Gene]
  • LOC129934464:ATAC-STARR-seq lymphoblastoid silent region 11826 [Gene]
  • LOC126806282:BRD4-independent group 4 enhancer GRCh37_chr2:100483776-100484975 [Gene]
  • LOC126806287:BRD4-independent group 4 enhancer GRCh37_chr2:102080348-102081547 [Gene]
  • CNOT11:CCR4-NOT transcription complex subunit 11 [Gene - OMIM - HGNC]
  • LOC126806281:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:100019841-100021040 [Gene]
  • CRACDL:CRACD like [Gene - HGNC]
  • LONRF2:LON peptidase N-terminal domain and ring finger 2 [Gene - HGNC]
  • LOC126806284:MED14-independent group 3 enhancer GRCh37_chr2:101518843-101520042 [Gene]
  • LOC126806286:MED14-independent group 3 enhancer GRCh37_chr2:101775410-101776609 [Gene]
  • LOC126806280:MED14-independent group 3 enhancer GRCh37_chr2:99656987-99658186 [Gene]
  • LOC129388892:MPRA-validated peak3796 silencer [Gene]
  • LOC129388893:MPRA-validated peak3800 silencer [Gene]
  • LOC129388894:MPRA-validated peak3801 silencer [Gene]
  • LOC120961776:NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:101946330-101947106 and GRCh37_chr2:101947107-101947883 [Gene]
  • NPAS2-AS1:NPAS2 antisense RNA 1 [Gene - HGNC]
  • LOC126806283:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:100865373-100866572 [Gene]
  • LOC126806285:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:101740925-101742124 [Gene]
  • LOC126806279:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:99051832-99053031 [Gene]
  • REV1:REV1 DNA directed polymerase [Gene - OMIM - HGNC]
  • LOC120961775:Sharpr-MPRA regulatory region 12407 [Gene]
  • LOC122817713:Sharpr-MPRA regulatory region 13812 [Gene]
  • LOC122817714:Sharpr-MPRA regulatory region 14605 [Gene]
  • LOC122817716:Sharpr-MPRA regulatory region 3478 [Gene]
  • LOC122817715:Sharpr-MPRA regulatory region 6151 [Gene]
  • LOC120961774:Sharpr-MPRA regulatory region 9249 [Gene]
  • TBC1D8:TBC1 domain family member 8 [Gene - HGNC]
  • TBC1D8-AS1:TBC1D8 antisense RNA 1 [Gene - HGNC]
  • LOC110121226:VISTA enhancer hs1933 [Gene]
  • MGAT4A:alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A [Gene - OMIM - HGNC]
  • CHST10:carbohydrate sulfotransferase 10 [Gene - OMIM - HGNC]
  • CREG2:cellular repressor of E1A stimulated genes 2 [Gene - OMIM - HGNC]
  • C2orf15:chromosome 2 open reading frame 15 [Gene - HGNC]
  • COA5:cytochrome c oxidase assembly factor 5 [Gene - OMIM - HGNC]
  • EIF5B:eukaryotic translation initiation factor 5B [Gene - OMIM - HGNC]
  • FRA2A:fragile site, folic acid type, rare, fra(2)(q11.2) [Gene - HGNC]
  • INPP4A:inositol polyphosphate-4-phosphatase type I A [Gene - OMIM - HGNC]
  • LIPT1:lipoyltransferase 1 [Gene - OMIM - HGNC]
  • LINC01104:long intergenic non-protein coding RNA 1104 [Gene - HGNC]
  • LINC01849:long intergenic non-protein coding RNA 1849 [Gene - HGNC]
  • LINC02611:long intergenic non-protein coding RNA 2611 [Gene - HGNC]
  • LYG1:lysozyme g1 [Gene - HGNC]
  • LYG2:lysozyme g2 [Gene - OMIM - HGNC]
  • MIR5696:microRNA 5696 [Gene - HGNC]
  • MITD1:microtubule interacting and trafficking domain containing 1 [Gene - HGNC]
  • MRPL30:mitochondrial ribosomal protein L30 [Gene - OMIM - HGNC]
  • NMS:neuromedin S [Gene - OMIM - HGNC]
  • NPAS2:neuronal PAS domain protein 2 [Gene - OMIM - HGNC]
  • PDCL3:phosducin like 3 [Gene - OMIM - HGNC]
  • RFX8:regulatory factor X8 [Gene - HGNC]
  • RPL31:ribosomal protein L31 [Gene - OMIM - HGNC]
  • RNF149:ring finger protein 149 [Gene - HGNC]
  • SNORD89:small nucleolar RNA, C/D box 89 [Gene - HGNC]
  • TSGA10:testis specific 10 [Gene - OMIM - HGNC]
  • TXNDC9:thioredoxin domain containing 9 [Gene - OMIM - HGNC]
  • UNC50:unc-50 inner nuclear membrane RNA binding protein [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
2q11.2
Genomic location:
Preferred name:
GRCh38/hg38 2q11.2(chr2:98411773-101636907)x1
HGVS:
  • NC_000002.12:g.(?_98411773)_(101636907_?)del
  • NC_000002.10:g.(?_98394668)_(101619801_?)del
  • NC_000002.11:g.(?_99028236)_(102253369_?)del
Links:
dbVar: nssv1603387; dbVar: nsv916605
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000179718ISCA site 1

See additional submitters

no assertion criteria provided
Likely pathogenic
(Oct 7, 2011) 		de novoclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot providednot providednot providedclinical 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, SCV000179718.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024