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GRCh38/hg38 1p33-32.3(chr1:50441439-50959811)x2 AND Orofacial cleft 13

Germline classification:
association (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:
RCV002488680.1

Allele description [Variation Report for GRCh38/hg38 1p33-32.3(chr1:50441439-50959811)x2]

GRCh38/hg38 1p33-32.3(chr1:50441439-50959811)x2

Genes:
  • AGBL4:AGBL carboxypeptidase 4 [Gene - OMIM - HGNC]
  • AGBL4-AS1:AGBL4 antisense RNA 1 [Gene - HGNC]
  • AGBL4-IT1:AGBL4 intronic transcript 1 [Gene - HGNC]
  • LOC129930503:ATAC-STARR-seq lymphoblastoid active region 1011 [Gene]
  • LOC129930505:ATAC-STARR-seq lymphoblastoid active region 1012 [Gene]
  • LOC129930509:ATAC-STARR-seq lymphoblastoid active region 1013 [Gene]
  • LOC129930511:ATAC-STARR-seq lymphoblastoid active region 1014 [Gene]
  • LOC129930512:ATAC-STARR-seq lymphoblastoid active region 1015 [Gene]
  • LOC129930513:ATAC-STARR-seq lymphoblastoid active region 1016 [Gene]
  • LOC129930514:ATAC-STARR-seq lymphoblastoid active region 1017 [Gene]
  • LOC129930518:ATAC-STARR-seq lymphoblastoid active region 1018 [Gene]
  • LOC129930524:ATAC-STARR-seq lymphoblastoid active region 1019 [Gene]
  • LOC129930525:ATAC-STARR-seq lymphoblastoid active region 1020 [Gene]
  • LOC129930526:ATAC-STARR-seq lymphoblastoid active region 1021 [Gene]
  • LOC129930527:ATAC-STARR-seq lymphoblastoid active region 1022 [Gene]
  • LOC129930529:ATAC-STARR-seq lymphoblastoid active region 1023 [Gene]
  • LOC129930530:ATAC-STARR-seq lymphoblastoid active region 1024 [Gene]
  • LOC129930531:ATAC-STARR-seq lymphoblastoid active region 1025 [Gene]
  • LOC129930532:ATAC-STARR-seq lymphoblastoid active region 1026 [Gene]
  • LOC129930534:ATAC-STARR-seq lymphoblastoid active region 1029 [Gene]
  • LOC129930536:ATAC-STARR-seq lymphoblastoid active region 1030 [Gene]
  • LOC129930540:ATAC-STARR-seq lymphoblastoid active region 1031 [Gene]
  • LOC129930543:ATAC-STARR-seq lymphoblastoid active region 1032 [Gene]
  • LOC129930544:ATAC-STARR-seq lymphoblastoid active region 1033 [Gene]
  • LOC129930552:ATAC-STARR-seq lymphoblastoid active region 1034 [Gene]
  • LOC129930553:ATAC-STARR-seq lymphoblastoid active region 1035 [Gene]
  • LOC129930555:ATAC-STARR-seq lymphoblastoid active region 1036 [Gene]
  • LOC129930504:ATAC-STARR-seq lymphoblastoid silent region 863 [Gene]
  • LOC129930506:ATAC-STARR-seq lymphoblastoid silent region 864 [Gene]
  • LOC129930507:ATAC-STARR-seq lymphoblastoid silent region 865 [Gene]
  • LOC129930508:ATAC-STARR-seq lymphoblastoid silent region 866 [Gene]
  • LOC129930510:ATAC-STARR-seq lymphoblastoid silent region 867 [Gene]
  • LOC129930515:ATAC-STARR-seq lymphoblastoid silent region 868 [Gene]
  • LOC129930516:ATAC-STARR-seq lymphoblastoid silent region 869 [Gene]
  • LOC129930517:ATAC-STARR-seq lymphoblastoid silent region 870 [Gene]
  • LOC129930519:ATAC-STARR-seq lymphoblastoid silent region 871 [Gene]
  • LOC129930520:ATAC-STARR-seq lymphoblastoid silent region 872 [Gene]
  • LOC129930521:ATAC-STARR-seq lymphoblastoid silent region 873 [Gene]
  • LOC129930522:ATAC-STARR-seq lymphoblastoid silent region 874 [Gene]
  • LOC129930523:ATAC-STARR-seq lymphoblastoid silent region 875 [Gene]
  • LOC129930528:ATAC-STARR-seq lymphoblastoid silent region 876 [Gene]
  • LOC129930533:ATAC-STARR-seq lymphoblastoid silent region 881 [Gene]
  • LOC129930535:ATAC-STARR-seq lymphoblastoid silent region 883 [Gene]
  • LOC129930537:ATAC-STARR-seq lymphoblastoid silent region 885 [Gene]
  • LOC129930538:ATAC-STARR-seq lymphoblastoid silent region 886 [Gene]
  • LOC129930539:ATAC-STARR-seq lymphoblastoid silent region 887 [Gene]
  • LOC129930541:ATAC-STARR-seq lymphoblastoid silent region 888 [Gene]
  • LOC129930542:ATAC-STARR-seq lymphoblastoid silent region 889 [Gene]
  • LOC129930545:ATAC-STARR-seq lymphoblastoid silent region 890 [Gene]
  • LOC129930546:ATAC-STARR-seq lymphoblastoid silent region 891 [Gene]
  • LOC129930547:ATAC-STARR-seq lymphoblastoid silent region 892 [Gene]
  • LOC129930548:ATAC-STARR-seq lymphoblastoid silent region 893 [Gene]
  • LOC129930549:ATAC-STARR-seq lymphoblastoid silent region 894 [Gene]
  • LOC129930550:ATAC-STARR-seq lymphoblastoid silent region 895 [Gene]
  • LOC129930551:ATAC-STARR-seq lymphoblastoid silent region 896 [Gene]
  • LOC129930554:ATAC-STARR-seq lymphoblastoid silent region 897 [Gene]
  • LOC129930556:ATAC-STARR-seq lymphoblastoid silent region 898 [Gene]
  • BEND5:BEN domain containing 5 [Gene - HGNC]
  • LOC115801428:CRISPRi-validated cis-regulatory element chr1.6035 [Gene]
  • DMRTA2:DMRT like family A2 [Gene - OMIM - HGNC]
  • ELAVL4:ELAV like RNA binding protein 4 [Gene - OMIM - HGNC]
  • EPS15-AS1:EPS15 antisense RNA 1 [Gene - HGNC]
  • FAF1-AS1:FAF1 antisense RNA 1 [Gene - HGNC]
  • FAF1:Fas associated factor 1 [Gene - OMIM - HGNC]
  • KTI12:KTI12 chromatin associated homolog [Gene - HGNC]
  • LOC126805730:MED14-independent group 3 enhancer GRCh37_chr1:51069018-51070217 [Gene]
  • LOC126805731:MED14-independent group 3 enhancer GRCh37_chr1:52087823-52089022 [Gene]
  • LOC126805733:MED14-independent group 3 enhancer GRCh37_chr1:52869594-52870793 [Gene]
  • LOC129388513:MPRA-validated peak211 silencer [Gene]
  • LOC129388514:MPRA-validated peak214 silencer [Gene]
  • LOC129388515:MPRA-validated peak217 silencer [Gene]
  • LOC129388516:MPRA-validated peak220 silencer [Gene]
  • LOC129388517:MPRA-validated peak222 silencer [Gene]
  • LOC129388518:MPRA-validated peak223 silencer [Gene]
  • LOC129388519:MPRA-validated peak224 silencer [Gene]
  • LOC129388520:MPRA-validated peak225 silencer [Gene]
  • LOC129388521:MPRA-validated peak226 silencer [Gene]
  • LOC129388522:MPRA-validated peak227 silencer [Gene]
  • LOC129388523:MPRA-validated peak228 silencer [Gene]
  • LOC129388524:MPRA-validated peak230 silencer [Gene]
  • LOC121725022:NANOG-H3K27ac hESC enhancers GRCh37_chr1:52815874-52816848 and GRCh37_chr1:52816849-52817822 [Gene]
  • LOC126805732:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:52362999-52364198 [Gene]
  • RAB3B:RAB3B, member RAS oncogene family [Gene - OMIM - HGNC]
  • LOC122056874:Sharpr-MPRA regulatory region 13275 [Gene]
  • LOC122056872:Sharpr-MPRA regulatory region 15542 [Gene]
  • LOC112590804:Sharpr-MPRA regulatory region 2435 [Gene]
  • LOC122056871:Sharpr-MPRA regulatory region 3774 [Gene]
  • LOC122056870:Sharpr-MPRA regulatory region 5693 [Gene]
  • LOC112590802:Sharpr-MPRA regulatory region 5937 [Gene]
  • LOC122056869:Sharpr-MPRA regulatory region 6511 [Gene]
  • LOC112590801:Sharpr-MPRA regulatory region 673 [Gene]
  • LOC122056873:Sharpr-MPRA regulatory region 753 [Gene]
  • LOC112590803:Sharpr-MPRA regulatory region 8174 [Gene]
  • TTC39A-AS1:TTC39A antisense RNA 1 [Gene - HGNC]
  • TXNDC12-AS1:TXNDC12 antisense RNA 1 [Gene - HGNC]
  • LOC110120607:VISTA enhancer hs194 [Gene]
  • LOC110120609:VISTA enhancer hs200 [Gene]
  • BTF3L4:basic transcription factor 3 like 4 [Gene - HGNC]
  • C1orf185:chromosome 1 open reading frame 185 [Gene - HGNC]
  • CC2D1B:coiled-coil and C2 domain containing 1B [Gene - HGNC]
  • CDKN2C:cyclin dependent kinase inhibitor 2C [Gene - OMIM - HGNC]
  • COA7:cytochrome c oxidase assembly factor 7 [Gene - OMIM - HGNC]
  • EPS15:epidermal growth factor receptor pathway substrate 15 [Gene - OMIM - HGNC]
  • GPX7:glutathione peroxidase 7 [Gene - OMIM - HGNC]
  • LOC107992392:heart enhancer 18 [Gene]
  • LINC01562:long intergenic non-protein coding RNA 1562 [Gene - HGNC]
  • LINC02808:long intergenic non-protein coding RNA 2808 [Gene - HGNC]
  • MIR4421:microRNA 4421 [Gene - HGNC]
  • MIR6500:microRNA 6500 [Gene - HGNC]
  • MIR761:microRNA 761 [Gene - HGNC]
  • NRDC:nardilysin convertase [Gene - OMIM - HGNC]
  • ORC1:origin recognition complex subunit 1 [Gene - OMIM - HGNC]
  • OSBPL9:oxysterol binding protein like 9 [Gene - OMIM - HGNC]
  • PRPF38A:pre-mRNA processing factor 38A [Gene - OMIM - HGNC]
  • RNF11:ring finger protein 11 [Gene - OMIM - HGNC]
  • SHISAL2A:shisa like 2A [Gene - OMIM - HGNC]
  • TUT4:terminal uridylyl transferase 4 [Gene - OMIM - HGNC]
  • TTC39A:tetratricopeptide repeat domain 39A [Gene - OMIM - HGNC]
  • TXNDC12:thioredoxin domain containing 12 [Gene - OMIM - HGNC]
  • ZFYVE9:zinc finger FYVE-type containing 9 [Gene - OMIM - HGNC]
  • ZYG11B:zyg-11 family member B, cell cycle regulator [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
1p33-32.3
Genomic location:
Chr1: 48666286 - 52808894 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 1p33-32.3(chr1:50441439-50959811)x2
HGVS:
    Functional consequence:
    loss of heterozygosity [Sequence Ontology: SO:0001786]

    Condition(s)

    Name:
    Orofacial cleft 13 (OFC13)
    Identifiers:
    MONDO: MONDO:0013466; MedGen: C3151222; OMIM: 613857

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV002758749Craniofacial science Laboratory, School of Dental Sciences, universiti sains malaysia
    no assertion criteria provided
    		associationunknownresearch

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    Malayunknownyes4not providednot providednot providednot providedresearch

    Citations

    PMC

    FAF1, a Gene that Is Disrupted in Cleft Palate and Has Conserved Function in Zebrafish.

    Ghassibe-Sabbagh M, Desmyter L, Langenberg T, Claes F, Boute O, Bayet B, Pellerin P, Hermans K, Backx L, Mansilla MA, Imoehl S, Nowak S, Ludwig KU, Baluardo C, Ferrian M, Mossey PA, Noethen M, Dewerchin M, François G, Revencu N, Vanwijck R, Hecht J, Mangold E, Murray J, Rubini M, Vermeesch JR, Poirel HA, Carmeliet P, Vikkula M.

    American Journal of Human Genetics. 2011 Feb 11; 88(2): 150-161

    PMC [article]
    PMCID:
    PMC3035709
    PMID:
    21295280
    DOI:
    10.1016/j.ajhg.2011.01.003

    Details of each submission

    From Craniofacial science Laboratory, School of Dental Sciences, universiti sains malaysia, SCV002758749.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1Malay4not providednot providedresearchnot provided

    Description

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

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1unknownyesnot providednot providednot provided4not providednot providednot provided

    Last Updated: Sep 1, 2024