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GRCh38/hg38 6p12.1-11.2(chr6:55755662-55874865)x2 AND Orofacial cleft

Germline classification:
Uncertain significance (1 submission)
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:
RCV002481089.3

Allele description [Variation Report for GRCh38/hg38 6p12.1-11.2(chr6:55755662-55874865)x2]

GRCh38/hg38 6p12.1-11.2(chr6:55755662-55874865)x2

Genes:
  • HMGCLL1:3-hydroxy-3-methylglutaryl-CoA lyase like 1 [Gene - OMIM - HGNC]
  • 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]
  • LOC129996656:ATAC-STARR-seq lymphoblastoid active region 24702 [Gene]
  • LOC129996657:ATAC-STARR-seq lymphoblastoid active region 24703 [Gene]
  • LOC129996659:ATAC-STARR-seq lymphoblastoid active region 24704 [Gene]
  • LOC129996660:ATAC-STARR-seq lymphoblastoid active region 24705 [Gene]
  • LOC129996661:ATAC-STARR-seq lymphoblastoid active region 24706 [Gene]
  • LOC129996662:ATAC-STARR-seq lymphoblastoid active region 24707 [Gene]
  • LOC129996664:ATAC-STARR-seq lymphoblastoid active region 24708 [Gene]
  • LOC129996668:ATAC-STARR-seq lymphoblastoid active region 24710 [Gene]
  • LOC129996669:ATAC-STARR-seq lymphoblastoid active region 24711 [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]
  • LOC129996658:ATAC-STARR-seq lymphoblastoid silent region 17296 [Gene]
  • LOC129996663:ATAC-STARR-seq lymphoblastoid silent region 17300 [Gene]
  • LOC129996665:ATAC-STARR-seq lymphoblastoid silent region 17302 [Gene]
  • LOC129996666:ATAC-STARR-seq lymphoblastoid silent region 17304 [Gene]
  • LOC129996667:ATAC-STARR-seq lymphoblastoid silent region 17305 [Gene]
  • BAG2:BAG cochaperone 2 [Gene - OMIM - HGNC]
  • BEND6:BEN domain containing 6 [Gene - HGNC]
  • LOC126088080:BRD4-independent group 4 enhancer GRCh37_chr6:58146291-58147490 [Gene]
  • LOC126859697:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:53989184-53990383 [Gene]
  • PRIM2:DNA primase subunit 2 [Gene - OMIM - HGNC]
  • DST-AS1:DST antisense RNA 1 [Gene - HGNC]
  • ELOVL5:ELOVL fatty acid elongase 5 [Gene - OMIM - HGNC]
  • GCLC-AS1:GCLC antisense RNA 1 [Gene - HGNC]
  • GFRAL:GDNF family receptor alpha like [Gene - OMIM - HGNC]
  • KIAA1586:KIAA1586 [Gene - HGNC]
  • KILH:KRT19 interacting long noncoding RNA in hepatocellular carcinoma [Gene - HGNC]
  • MLIP-AS1:MLIP antisense RNA 1 [Gene - HGNC]
  • MLIP-IT1:MLIP intronic transcript 1 [Gene - HGNC]
  • LOC129389544:MPRA-validated peak5860 silencer [Gene]
  • LOC129389545:MPRA-validated peak5861 silencer [Gene]
  • LOC132089408:Neanderthal introgressed variant-containing enhancer experimental_92170 [Gene]
  • LOC132089409:Neanderthal introgressed variant-containing enhancer experimental_92203 [Gene]
  • LOC132089410:Neanderthal introgressed variant-containing enhancer experimental_92273 [Gene]
  • LOC132089411:Neanderthal introgressed variant-containing enhancer experimental_92293 [Gene]
  • LOC132090757:Neanderthal introgressed variant-containing enhancer experimental_92361 [Gene]
  • LOC132089412:Neanderthal introgressed variant-containing enhancer experimental_92363 [Gene]
  • LOC132089413:Neanderthal introgressed variant-containing enhancer experimental_92364 [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]
  • LOC126859698:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:56803197-56804396 [Gene]
  • RAB23:RAB23, member RAS oncogene family [Gene - OMIM - HGNC]
  • LOC121740652:Sharpr-MPRA regulatory region 10125 [Gene]
  • LOC123744827:Sharpr-MPRA regulatory region 10889 [Gene]
  • LOC113175007:Sharpr-MPRA regulatory region 11274 [Gene]
  • LOC123744830:Sharpr-MPRA regulatory region 11401 [Gene]
  • LOC123744826:Sharpr-MPRA regulatory region 14005 [Gene]
  • LOC121132689:Sharpr-MPRA regulatory region 2673 [Gene]
  • LOC121740653:Sharpr-MPRA regulatory region 3486 [Gene]
  • LOC123744825:Sharpr-MPRA regulatory region 4240 [Gene]
  • LOC123744829:Sharpr-MPRA regulatory region 6371 [Gene]
  • LOC123744828:Sharpr-MPRA regulatory region 6720 [Gene]
  • LOC123744831:Sharpr-MPRA regulatory region 7771 [Gene]
  • ZNF451-AS1:ZNF451 regulatory antisense RNA 1 [Gene - HGNC]
  • BMP5:bone morphogenetic protein 5 [Gene - OMIM - HGNC]
  • COL21A1:collagen type XXI alpha 1 chain [Gene - OMIM - HGNC]
  • DST:dystonin [Gene - OMIM - HGNC]
  • FAM83B:family with sequence similarity 83 member B [Gene - HGNC]
  • GCLC:glutamate-cysteine ligase catalytic subunit [Gene - OMIM - HGNC]
  • HCRTR2:hypocretin receptor 2 [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]
  • LINC03001:long intergenic non-protein coding RNA 3001 [Gene - HGNC]
  • LINC00680:long intergenic non-protein coding RNA 680 [Gene - HGNC]
  • MIR548U:microRNA 548u [Gene - HGNC]
  • MIR5685:microRNA 5685 [Gene - HGNC]
  • MLIP:muscular LMNA interacting protein [Gene - OMIM - HGNC]
  • TRA-AGC12-3:tRNA-Ala (anticodon AGC) 12-3 [Gene - HGNC]
  • TRA-AGC13-2:tRNA-Ala (anticodon AGC) 13-2 [Gene - HGNC]
  • TRA-AGC16-1:tRNA-Ala (anticodon AGC) 16-1 [Gene - HGNC]
  • TRA-AGC24-1:tRNA-Ala (anticodon AGC) 24-1 [Gene - HGNC]
  • TRI-AAT1-1:tRNA-Ile (anticodon AAT) 1-1 [Gene - HGNC]
  • TRM-CAT7-1:tRNA-Met (anticodon CAT) 7-1 [Gene - HGNC]
  • TINAG:tubulointerstitial nephritis antigen [Gene - OMIM - HGNC]
  • LOC101927189:uncharacterized LOC101927189 [Gene]
  • LOC101927293:uncharacterized LOC101927293 [Gene]
  • ZNF451:zinc finger protein 451 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
6p12.1-11.2
Genomic location:
Chr6: 53151508 - 58400428 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 6p12.1-11.2(chr6:55755662-55874865)x2
HGVS:
    Functional consequence:
    loss of heterozygosity [Sequence Ontology: SO:0001786]

    Condition(s)

    Name:
    Orofacial cleft
    Synonyms:
    Orofacial clefting; Oral cleft
    Identifiers:
    MONDO: MONDO:0000358; MedGen: C3266076; OMIM: PS119530; Human Phenotype Ontology: HP:0000202

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV002758752Craniofacial science Laboratory, School of Dental Sciences, universiti sains malaysia
    no assertion criteria provided
    		Uncertain significanceunknownresearch

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    Malayunknownyes3not providednot providednot providednot providedresearch

    Citations

    PMC

    Microsatellite markers: what they mean and why they are so useful.

    Vieira ML, Santini L, Diniz AL, Munhoz CD.

    Genetics and Molecular Biology. 2016 Aug 4; 39(3): 312-328

    PMC [article]
    PMCID:
    PMC5004837
    PMID:
    27561112
    DOI:
    10.1590/1678-4685-GMB-2016-0027

    Details of each submission

    From Craniofacial science Laboratory, School of Dental Sciences, universiti sains malaysia, SCV002758752.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1Malay3not providednot providedresearchnot provided

    Description

    In NSCL/P subjects, loss of peaks at 141 bp indicated loss one allele and are scored as loss of heterozygosity (LOH).

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1unknownyesnot providednot providednot provided3not providednot providednot provided

    Last Updated: Dec 2, 2023