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GRCh38/hg38 6p21.1-12.1(chr6:45681671-54212044)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 20, 2012
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:
RCV000138349.6

Allele description

GRCh38/hg38 6p21.1-12.1(chr6:45681671-54212044)x1

Genes:
  • ADGRF5-AS1:ADGRF5 antisense RNA 1 [Gene - HGNC]
  • LOC129996581:ATAC-STARR-seq lymphoblastoid active region 24646 [Gene]
  • LOC129996583:ATAC-STARR-seq lymphoblastoid active region 24647 [Gene]
  • LOC129996584:ATAC-STARR-seq lymphoblastoid active region 24648 [Gene]
  • LOC129996585:ATAC-STARR-seq lymphoblastoid active region 24649 [Gene]
  • LOC129996586:ATAC-STARR-seq lymphoblastoid active region 24650 [Gene]
  • LOC129996588:ATAC-STARR-seq lymphoblastoid active region 24651 [Gene]
  • LOC129996591:ATAC-STARR-seq lymphoblastoid active region 24652 [Gene]
  • LOC129996592:ATAC-STARR-seq lymphoblastoid active region 24653 [Gene]
  • LOC129996594:ATAC-STARR-seq lymphoblastoid active region 24654 [Gene]
  • LOC129996596:ATAC-STARR-seq lymphoblastoid active region 24655 [Gene]
  • LOC129996597:ATAC-STARR-seq lymphoblastoid active region 24656 [Gene]
  • LOC129996598:ATAC-STARR-seq lymphoblastoid active region 24657 [Gene]
  • LOC129996599:ATAC-STARR-seq lymphoblastoid active region 24658 [Gene]
  • LOC129996600:ATAC-STARR-seq lymphoblastoid active region 24659 [Gene]
  • LOC129996601:ATAC-STARR-seq lymphoblastoid active region 24660 [Gene]
  • LOC129996602:ATAC-STARR-seq lymphoblastoid active region 24661 [Gene]
  • LOC129996603:ATAC-STARR-seq lymphoblastoid active region 24662 [Gene]
  • LOC129996607:ATAC-STARR-seq lymphoblastoid active region 24664 [Gene]
  • LOC129996608:ATAC-STARR-seq lymphoblastoid active region 24665 [Gene]
  • LOC129996610:ATAC-STARR-seq lymphoblastoid active region 24666 [Gene]
  • LOC129996611:ATAC-STARR-seq lymphoblastoid active region 24667 [Gene]
  • LOC129996612:ATAC-STARR-seq lymphoblastoid active region 24668 [Gene]
  • LOC129996613:ATAC-STARR-seq lymphoblastoid active region 24669 [Gene]
  • LOC129996614:ATAC-STARR-seq lymphoblastoid active region 24670 [Gene]
  • LOC129996615:ATAC-STARR-seq lymphoblastoid active region 24671 [Gene]
  • LOC129996617:ATAC-STARR-seq lymphoblastoid active region 24672 [Gene]
  • LOC129996619:ATAC-STARR-seq lymphoblastoid active region 24673 [Gene]
  • LOC129996622:ATAC-STARR-seq lymphoblastoid active region 24674 [Gene]
  • LOC129996624:ATAC-STARR-seq lymphoblastoid active region 24676 [Gene]
  • LOC129996625:ATAC-STARR-seq lymphoblastoid active region 24678 [Gene]
  • LOC129996626:ATAC-STARR-seq lymphoblastoid active region 24679 [Gene]
  • LOC129996627:ATAC-STARR-seq lymphoblastoid active region 24680 [Gene]
  • LOC129996628:ATAC-STARR-seq lymphoblastoid active region 24681 [Gene]
  • LOC129996629:ATAC-STARR-seq lymphoblastoid active region 24682 [Gene]
  • LOC129996630:ATAC-STARR-seq lymphoblastoid active region 24683 [Gene]
  • LOC129996631:ATAC-STARR-seq lymphoblastoid active region 24684 [Gene]
  • LOC129996632:ATAC-STARR-seq lymphoblastoid active region 24685 [Gene]
  • LOC129996633:ATAC-STARR-seq lymphoblastoid active region 24686 [Gene]
  • LOC129996636:ATAC-STARR-seq lymphoblastoid active region 24687 [Gene]
  • LOC129996637:ATAC-STARR-seq lymphoblastoid active region 24688 [Gene]
  • LOC129996638:ATAC-STARR-seq lymphoblastoid active region 24689 [Gene]
  • LOC129996640:ATAC-STARR-seq lymphoblastoid active region 24690 [Gene]
  • LOC129996641:ATAC-STARR-seq lymphoblastoid active region 24693 [Gene]
  • LOC129996644:ATAC-STARR-seq lymphoblastoid active region 24694 [Gene]
  • LOC129996645:ATAC-STARR-seq lymphoblastoid active region 24695 [Gene]
  • LOC129996646:ATAC-STARR-seq lymphoblastoid active region 24696 [Gene]
  • LOC129996647:ATAC-STARR-seq lymphoblastoid active region 24697 [Gene]
  • LOC129996651:ATAC-STARR-seq lymphoblastoid active region 24699 [Gene]
  • LOC129996652:ATAC-STARR-seq lymphoblastoid active region 24700 [Gene]
  • LOC129996582:ATAC-STARR-seq lymphoblastoid silent region 17267 [Gene]
  • LOC129996587:ATAC-STARR-seq lymphoblastoid silent region 17269 [Gene]
  • LOC129996589:ATAC-STARR-seq lymphoblastoid silent region 17270 [Gene]
  • LOC129996590:ATAC-STARR-seq lymphoblastoid silent region 17271 [Gene]
  • LOC129996593:ATAC-STARR-seq lymphoblastoid silent region 17272 [Gene]
  • LOC129996595:ATAC-STARR-seq lymphoblastoid silent region 17273 [Gene]
  • LOC129996604:ATAC-STARR-seq lymphoblastoid silent region 17275 [Gene]
  • LOC129996605:ATAC-STARR-seq lymphoblastoid silent region 17276 [Gene]
  • LOC129996606:ATAC-STARR-seq lymphoblastoid silent region 17277 [Gene]
  • LOC129996609:ATAC-STARR-seq lymphoblastoid silent region 17278 [Gene]
  • LOC129996616:ATAC-STARR-seq lymphoblastoid silent region 17279 [Gene]
  • LOC129996618:ATAC-STARR-seq lymphoblastoid silent region 17280 [Gene]
  • LOC129996620:ATAC-STARR-seq lymphoblastoid silent region 17281 [Gene]
  • LOC129996621:ATAC-STARR-seq lymphoblastoid silent region 17282 [Gene]
  • LOC129996623:ATAC-STARR-seq lymphoblastoid silent region 17283 [Gene]
  • LOC129996634:ATAC-STARR-seq lymphoblastoid silent region 17284 [Gene]
  • LOC129996635:ATAC-STARR-seq lymphoblastoid silent region 17285 [Gene]
  • LOC129996639:ATAC-STARR-seq lymphoblastoid silent region 17286 [Gene]
  • LOC129996642:ATAC-STARR-seq lymphoblastoid silent region 17287 [Gene]
  • LOC129996643:ATAC-STARR-seq lymphoblastoid silent region 17288 [Gene]
  • LOC129996648:ATAC-STARR-seq lymphoblastoid silent region 17289 [Gene]
  • LOC129996649:ATAC-STARR-seq lymphoblastoid silent region 17291 [Gene]
  • LOC129996650:ATAC-STARR-seq lymphoblastoid silent region 17292 [Gene]
  • LOC129996653:ATAC-STARR-seq lymphoblastoid silent region 17293 [Gene]
  • LOC129996654:ATAC-STARR-seq lymphoblastoid silent region 17294 [Gene]
  • LOC129996655:ATAC-STARR-seq lymphoblastoid silent region 17295 [Gene]
  • LOC126859683:BRD4-independent group 4 enhancer GRCh37_chr6:46894113-46895312 [Gene]
  • LOC126859684:BRD4-independent group 4 enhancer GRCh37_chr6:47011981-47013180 [Gene]
  • LOC126859691:BRD4-independent group 4 enhancer GRCh37_chr6:51961188-51962387 [Gene]
  • LOC126859693:BRD4-independent group 4 enhancer GRCh37_chr6:52577613-52578812 [Gene]
  • CD2AP:CD2 associated protein [Gene - OMIM - HGNC]
  • CD2AP-DT:CD2AP divergent transcript [Gene - HGNC]
  • LOC126859682:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:45868755-45869954 [Gene]
  • LOC126859689:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:49859209-49860408 [Gene]
  • LOC126859697:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:53989184-53990383 [Gene]
  • LOC116183064:CRISPRi-validated cis-regulatory element chr6.3292 [Gene]
  • EFHC1:EF-hand domain containing 1 [Gene - OMIM - HGNC]
  • ELOVL5:ELOVL fatty acid elongase 5 [Gene - OMIM - HGNC]
  • FBXO9:F-box protein 9 [Gene - OMIM - HGNC]
  • LOC111365194:FOXA motif-containing MPRA enhancer 62 [Gene]
  • LOC111429620:GATA motif-containing MPRA enhancer 217 [Gene]
  • GCLC-AS1:GCLC antisense RNA 1 [Gene - HGNC]
  • KILH:KRT19 interacting long noncoding RNA in hepatocellular carcinoma [Gene - HGNC]
  • LOC126859685:MED14-independent group 3 enhancer GRCh37_chr6:47252971-47254170 [Gene]
  • LOC126859686:MED14-independent group 3 enhancer GRCh37_chr6:47589053-47590252 [Gene]
  • LOC126859687:MED14-independent group 3 enhancer GRCh37_chr6:48078458-48079657 [Gene]
  • LOC126859690:MED14-independent group 3 enhancer GRCh37_chr6:51888848-51890047 [Gene]
  • MLIP-AS1:MLIP antisense RNA 1 [Gene - HGNC]
  • MLIP-IT1:MLIP intronic transcript 1 [Gene - HGNC]
  • LOC129389529:MPRA-validated peak5829 silencer [Gene]
  • LOC129389530:MPRA-validated peak5831 silencer [Gene]
  • LOC129389531:MPRA-validated peak5833 silencer [Gene]
  • LOC129389532:MPRA-validated peak5834 silencer [Gene]
  • LOC129389533:MPRA-validated peak5837 silencer [Gene]
  • LOC129389534:MPRA-validated peak5838 silencer [Gene]
  • LOC129389535:MPRA-validated peak5839 silencer [Gene]
  • LOC129389536:MPRA-validated peak5842 silencer [Gene]
  • LOC129389537:MPRA-validated peak5843 silencer [Gene]
  • LOC129389538:MPRA-validated peak5845 silencer [Gene]
  • LOC129389539:MPRA-validated peak5848 silencer [Gene]
  • LOC129389540:MPRA-validated peak5850 silencer [Gene]
  • LOC129389541:MPRA-validated peak5851 silencer [Gene]
  • LOC129389542:MPRA-validated peak5855 silencer [Gene]
  • LOC129389543:MPRA-validated peak5857 silencer [Gene]
  • LOC132089398:Neanderthal introgressed variant-containing enhancer experimental_92032 [Gene]
  • LOC132089399:Neanderthal introgressed variant-containing enhancer experimental_92072 [Gene]
  • LOC132090755:Neanderthal introgressed variant-containing enhancer experimental_92086 [Gene]
  • LOC132089400:Neanderthal introgressed variant-containing enhancer experimental_92132 [Gene]
  • LOC132089401:Neanderthal introgressed variant-containing enhancer experimental_92146 [Gene]
  • LOC132089402:Neanderthal introgressed variant-containing enhancer experimental_92147 [Gene]
  • LOC132089403:Neanderthal introgressed variant-containing enhancer experimental_92148 [Gene]
  • LOC132090756:Neanderthal introgressed variant-containing enhancer experimental_92149 [Gene]
  • LOC132089404:Neanderthal introgressed variant-containing enhancer experimental_92150 [Gene]
  • LOC132089405:Neanderthal introgressed variant-containing enhancer experimental_92153 [Gene]
  • LOC132089406:Neanderthal introgressed variant-containing enhancer experimental_92154 [Gene]
  • LOC132089407:Neanderthal introgressed variant-containing enhancer experimental_92160 [Gene]
  • LOC132089408:Neanderthal introgressed variant-containing enhancer experimental_92170 [Gene]
  • LOC132089409:Neanderthal introgressed variant-containing enhancer experimental_92203 [Gene]
  • LOC126859688:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:48794410-48795609 [Gene]
  • LOC121740649:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:50992467-50993666 [Gene]
  • LOC126859692:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:52368564-52369763 [Gene]
  • LOC126859694:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:53480209-53481408 [Gene]
  • LOC126859695:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:53599001-53600200 [Gene]
  • LOC126859696:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:53848425-53849624 [Gene]
  • PKHD1:PKHD1 ciliary IPT domain containing fibrocystin/polyductin [Gene - OMIM - HGNC]
  • RCAN2-DT:RCAN2 divergent transcript [Gene - HGNC]
  • RN7SK:RNA component of 7SK nuclear ribonucleoprotein [Gene - OMIM - HGNC]
  • RHAG:Rh associated glycoprotein [Gene - OMIM - HGNC]
  • LOC121740652:Sharpr-MPRA regulatory region 10125 [Gene]
  • LOC123744822:Sharpr-MPRA regulatory region 10279 [Gene]
  • LOC114004401:Sharpr-MPRA regulatory region 10363 [Gene]
  • LOC123744823:Sharpr-MPRA regulatory region 1037 [Gene]
  • LOC123744821:Sharpr-MPRA regulatory region 10484 [Gene]
  • LOC121740650:Sharpr-MPRA regulatory region 10632 [Gene]
  • LOC123744827:Sharpr-MPRA regulatory region 10889 [Gene]
  • LOC113175007:Sharpr-MPRA regulatory region 11274 [Gene]
  • LOC123744816:Sharpr-MPRA regulatory region 13557 [Gene]
  • LOC123744826:Sharpr-MPRA regulatory region 14005 [Gene]
  • LOC123744815:Sharpr-MPRA regulatory region 15024 [Gene]
  • LOC123744814:Sharpr-MPRA regulatory region 1586 [Gene]
  • LOC114004402:Sharpr-MPRA regulatory region 1859 [Gene]
  • LOC123744824:Sharpr-MPRA regulatory region 2296 [Gene]
  • LOC123744820:Sharpr-MPRA regulatory region 305 [Gene]
  • LOC123744817:Sharpr-MPRA regulatory region 3755 [Gene]
  • LOC121132687:Sharpr-MPRA regulatory region 4111 [Gene]
  • LOC123744825:Sharpr-MPRA regulatory region 4240 [Gene]
  • LOC123744819:Sharpr-MPRA regulatory region 4614 [Gene]
  • LOC121740651:Sharpr-MPRA regulatory region 5108 [Gene]
  • LOC113175006:Sharpr-MPRA regulatory region 5928 [Gene]
  • LOC123744818:Sharpr-MPRA regulatory region 6456 [Gene]
  • LOC123744828:Sharpr-MPRA regulatory region 6720 [Gene]
  • LOC121132688:Sharpr-MPRA regulatory region 8754 [Gene]
  • TDRD6-AS1:TDRD6 and SLC25A27 antisense RNA 1 [Gene - HGNC]
  • TNFRSF21:TNF receptor superfamily member 21 [Gene - OMIM - HGNC]
  • TRAM2-AS1:TRAM2 antisense RNA 1 (head to head) [Gene - HGNC]
  • LOC110121112:VISTA enhancer hs1461 [Gene]
  • LOC110121250:VISTA enhancer hs2064 [Gene]
  • LOC110120617:VISTA enhancer hs217 [Gene]
  • LOC110120792:VISTA enhancer hs865 [Gene]
  • ADGRF1:adhesion G protein-coupled receptor F1 [Gene - OMIM - HGNC]
  • ADGRF2:adhesion G protein-coupled receptor F2 [Gene - HGNC]
  • ADGRF4:adhesion G protein-coupled receptor F4 [Gene - OMIM - HGNC]
  • ADGRF5:adhesion G protein-coupled receptor F5 [Gene - HGNC]
  • ANKRD66:ankyrin repeat domain 66 [Gene - HGNC]
  • CENPQ:centromere protein Q [Gene - OMIM - HGNC]
  • CLIC5:chloride intracellular channel 5 [Gene - OMIM - HGNC]
  • C6orf141:chromosome 6 open reading frame 141 [Gene - HGNC]
  • CILK1:ciliogenesis associated kinase 1 [Gene - OMIM - HGNC]
  • CRISP1:cysteine rich secretory protein 1 [Gene - OMIM - HGNC]
  • CRISP2:cysteine rich secretory protein 2 [Gene - OMIM - HGNC]
  • CRISP3:cysteine rich secretory protein 3 [Gene - OMIM - HGNC]
  • CYP39A1:cytochrome P450 family 39 subfamily A member 1 [Gene - OMIM - HGNC]
  • DEFB110:defensin beta 110 [Gene - HGNC]
  • DEFB112:defensin beta 112 [Gene - HGNC]
  • DEFB113:defensin beta 113 [Gene - HGNC]
  • DEFB114:defensin beta 114 [Gene - OMIM - HGNC]
  • ENPP4:ectonucleotide pyrophosphatase/phosphodiesterase 4 [Gene - OMIM - HGNC]
  • ENPP5:ectonucleotide pyrophosphatase/phosphodiesterase family member 5 [Gene - OMIM - HGNC]
  • GCM1:glial cells missing transcription factor 1 [Gene - OMIM - HGNC]
  • GCLC:glutamate-cysteine ligase catalytic subunit [Gene - OMIM - HGNC]
  • GSTA1:glutathione S-transferase alpha 1 [Gene - OMIM - HGNC]
  • GSTA2:glutathione S-transferase alpha 2 [Gene - OMIM - HGNC]
  • GSTA3:glutathione S-transferase alpha 3 [Gene - OMIM - HGNC]
  • GSTA4:glutathione S-transferase alpha 4 [Gene - OMIM - HGNC]
  • GSTA5:glutathione S-transferase alpha 5 [Gene - OMIM - HGNC]
  • GLYATL3:glycine-N-acyltransferase like 3 [Gene - OMIM - HGNC]
  • IL17A:interleukin 17A [Gene - OMIM - HGNC]
  • IL17F:interleukin 17F [Gene - OMIM - HGNC]
  • KLHL31:kelch like family member 31 [Gene - OMIM - HGNC]
  • LRRC1:leucine rich repeat containing 1 [Gene - OMIM - HGNC]
  • LINC01564:long intergenic non-protein coding RNA 1564 [Gene - HGNC]
  • LINCMD1:long intergenic non-protein coding RNA, muscle differentiation 1 [Gene - OMIM - HGNC]
  • MEP1A:meprin A subunit alpha [Gene - OMIM - HGNC]
  • MMUT:methylmalonyl-CoA mutase [Gene - OMIM - HGNC]
  • MIR133B:microRNA 133b [Gene - OMIM - HGNC]
  • MIR206:microRNA 206 [Gene - OMIM - HGNC]
  • MIR5685:microRNA 5685 [Gene - HGNC]
  • MCM3:minichromosome maintenance complex component 3 [Gene - OMIM - HGNC]
  • MLIP:muscular LMNA interacting protein [Gene - OMIM - HGNC]
  • OPN5:opsin 5 [Gene - OMIM - HGNC]
  • PTCHD4:patched domain containing 4 [Gene - OMIM - HGNC]
  • PGK2:phosphoglycerate kinase 2 [Gene - OMIM - HGNC]
  • PLA2G7:phospholipase A2 group VII [Gene - OMIM - HGNC]
  • PAQR8:progestin and adipoQ receptor family member 8 [Gene - OMIM - HGNC]
  • RCAN2:regulator of calcineurin 2 [Gene - OMIM - HGNC]
  • SLC25A27:solute carrier family 25 member 27 [Gene - OMIM - HGNC]
  • TFAP2B:transcription factor AP-2 beta [Gene - OMIM - HGNC]
  • TFAP2D:transcription factor AP-2 delta [Gene - OMIM - HGNC]
  • TRAM2:translocation associated membrane protein 2 [Gene - OMIM - HGNC]
  • TMEM14A:transmembrane protein 14A [Gene - OMIM - HGNC]
  • TDRD6:tudor domain containing 6 [Gene - OMIM - HGNC]
  • LOC100505985:uncharacterized LOC100505985 [Gene]
  • LOC101926915:uncharacterized LOC101926915 [Gene]
  • LOC101927020:uncharacterized LOC101927020 [Gene]
  • LOC101927048:uncharacterized LOC101927048 [Gene]
  • LOC101927082:uncharacterized LOC101927082 [Gene]
  • LOC101927189:uncharacterized LOC101927189 [Gene]
  • LOC128031835:uncharacterized LOC128031835 [Gene]
  • LOC128092246:uncharacterized LOC128092246 [Gene]
  • LOC730101:uncharacterized LOC730101 [Gene]
Variant type:
copy number loss
Cytogenetic location:
6p21.1-12.1
Genomic location:
Preferred name:
GRCh38/hg38 6p21.1-12.1(chr6:45681671-54212044)x1
HGVS:
  • NC_000006.12:g.(?_45681671)_(54212044_?)del
  • NC_000006.10:g.(?_45757386)_(54184801_?)del
  • NC_000006.11:g.(?_45649408)_(54076842_?)del
Links:
dbVar: nssv1601470; dbVar: nsv915557
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
SCV000178632ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Aug 20, 2012) 		not providedclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
humannot providedyes1not 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, SCV000178632.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1human1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providedyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: Oct 14, 2023