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NC_000022.11:g.47513236_50806138del AND Phelan-McDermid syndrome

Germline classification:
Pathogenic (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:
RCV001254357.4

Allele description [Variation Report for NC_000022.11:g.47513236_50806138del]

NC_000022.11:g.47513236_50806138del

Genes:
  • ALG12:ALG12 alpha-1,6-mannosyltransferase [Gene - OMIM - HGNC]
  • LOC130067755:ATAC-STARR-seq lymphoblastoid active region 19270 [Gene]
  • LOC130067756:ATAC-STARR-seq lymphoblastoid active region 19271 [Gene]
  • LOC130067757:ATAC-STARR-seq lymphoblastoid active region 19272 [Gene]
  • LOC130067758:ATAC-STARR-seq lymphoblastoid active region 19273 [Gene]
  • LOC130067759:ATAC-STARR-seq lymphoblastoid active region 19274 [Gene]
  • LOC130067760:ATAC-STARR-seq lymphoblastoid active region 19275 [Gene]
  • LOC130067761:ATAC-STARR-seq lymphoblastoid active region 19276 [Gene]
  • LOC130067762:ATAC-STARR-seq lymphoblastoid active region 19277 [Gene]
  • LOC130067763:ATAC-STARR-seq lymphoblastoid active region 19279 [Gene]
  • LOC130067766:ATAC-STARR-seq lymphoblastoid active region 19280 [Gene]
  • LOC130067767:ATAC-STARR-seq lymphoblastoid active region 19281 [Gene]
  • LOC130067774:ATAC-STARR-seq lymphoblastoid active region 19282 [Gene]
  • LOC130067777:ATAC-STARR-seq lymphoblastoid active region 19284 [Gene]
  • LOC130067778:ATAC-STARR-seq lymphoblastoid active region 19285 [Gene]
  • LOC130067779:ATAC-STARR-seq lymphoblastoid active region 19286 [Gene]
  • LOC130067780:ATAC-STARR-seq lymphoblastoid active region 19287 [Gene]
  • LOC130067782:ATAC-STARR-seq lymphoblastoid active region 19288 [Gene]
  • LOC130067792:ATAC-STARR-seq lymphoblastoid active region 19289 [Gene]
  • LOC130067793:ATAC-STARR-seq lymphoblastoid active region 19290 [Gene]
  • LOC130067795:ATAC-STARR-seq lymphoblastoid active region 19291 [Gene]
  • LOC130067796:ATAC-STARR-seq lymphoblastoid active region 19292 [Gene]
  • LOC130067799:ATAC-STARR-seq lymphoblastoid active region 19293 [Gene]
  • LOC130067800:ATAC-STARR-seq lymphoblastoid active region 19294 [Gene]
  • LOC130067801:ATAC-STARR-seq lymphoblastoid active region 19295 [Gene]
  • LOC130067804:ATAC-STARR-seq lymphoblastoid active region 19296 [Gene]
  • LOC130067807:ATAC-STARR-seq lymphoblastoid active region 19297 [Gene]
  • LOC130067814:ATAC-STARR-seq lymphoblastoid active region 19298 [Gene]
  • LOC130067815:ATAC-STARR-seq lymphoblastoid active region 19299 [Gene]
  • LOC130067816:ATAC-STARR-seq lymphoblastoid active region 19300 [Gene]
  • LOC130067817:ATAC-STARR-seq lymphoblastoid active region 19302 [Gene]
  • LOC130067818:ATAC-STARR-seq lymphoblastoid active region 19303 [Gene]
  • LOC130067820:ATAC-STARR-seq lymphoblastoid active region 19304 [Gene]
  • LOC130067821:ATAC-STARR-seq lymphoblastoid active region 19305 [Gene]
  • LOC130067824:ATAC-STARR-seq lymphoblastoid active region 19306 [Gene]
  • LOC130067825:ATAC-STARR-seq lymphoblastoid active region 19307 [Gene]
  • LOC130067826:ATAC-STARR-seq lymphoblastoid active region 19309 [Gene]
  • LOC130067829:ATAC-STARR-seq lymphoblastoid active region 19311 [Gene]
  • LOC130067839:ATAC-STARR-seq lymphoblastoid active region 19312 [Gene]
  • LOC130067845:ATAC-STARR-seq lymphoblastoid active region 19314 [Gene]
  • LOC130067847:ATAC-STARR-seq lymphoblastoid active region 19316 [Gene]
  • LOC130067848:ATAC-STARR-seq lymphoblastoid active region 19317 [Gene]
  • LOC130067852:ATAC-STARR-seq lymphoblastoid active region 19318 [Gene]
  • LOC130067853:ATAC-STARR-seq lymphoblastoid active region 19319 [Gene]
  • LOC130067854:ATAC-STARR-seq lymphoblastoid active region 19320 [Gene]
  • LOC130067858:ATAC-STARR-seq lymphoblastoid active region 19321 [Gene]
  • LOC130067863:ATAC-STARR-seq lymphoblastoid active region 19324 [Gene]
  • LOC130067864:ATAC-STARR-seq lymphoblastoid active region 19325 [Gene]
  • LOC130067872:ATAC-STARR-seq lymphoblastoid active region 19326 [Gene]
  • LOC130067873:ATAC-STARR-seq lymphoblastoid active region 19328 [Gene]
  • LOC130067874:ATAC-STARR-seq lymphoblastoid active region 19329 [Gene]
  • LOC130067875:ATAC-STARR-seq lymphoblastoid active region 19330 [Gene]
  • LOC130067879:ATAC-STARR-seq lymphoblastoid active region 19331 [Gene]
  • LOC130067886:ATAC-STARR-seq lymphoblastoid active region 19332 [Gene]
  • LOC130067888:ATAC-STARR-seq lymphoblastoid active region 19333 [Gene]
  • LOC130067764:ATAC-STARR-seq lymphoblastoid silent region 13920 [Gene]
  • LOC130067765:ATAC-STARR-seq lymphoblastoid silent region 13921 [Gene]
  • LOC130067768:ATAC-STARR-seq lymphoblastoid silent region 13922 [Gene]
  • LOC130067769:ATAC-STARR-seq lymphoblastoid silent region 13923 [Gene]
  • LOC130067770:ATAC-STARR-seq lymphoblastoid silent region 13924 [Gene]
  • LOC130067771:ATAC-STARR-seq lymphoblastoid silent region 13925 [Gene]
  • LOC130067772:ATAC-STARR-seq lymphoblastoid silent region 13926 [Gene]
  • LOC130067773:ATAC-STARR-seq lymphoblastoid silent region 13927 [Gene]
  • LOC130067775:ATAC-STARR-seq lymphoblastoid silent region 13928 [Gene]
  • LOC130067776:ATAC-STARR-seq lymphoblastoid silent region 13929 [Gene]
  • LOC130067781:ATAC-STARR-seq lymphoblastoid silent region 13930 [Gene]
  • LOC130067783:ATAC-STARR-seq lymphoblastoid silent region 13931 [Gene]
  • LOC130067784:ATAC-STARR-seq lymphoblastoid silent region 13932 [Gene]
  • LOC130067785:ATAC-STARR-seq lymphoblastoid silent region 13935 [Gene]
  • LOC130067786:ATAC-STARR-seq lymphoblastoid silent region 13936 [Gene]
  • LOC130067787:ATAC-STARR-seq lymphoblastoid silent region 13937 [Gene]
  • LOC130067788:ATAC-STARR-seq lymphoblastoid silent region 13938 [Gene]
  • LOC130067789:ATAC-STARR-seq lymphoblastoid silent region 13939 [Gene]
  • LOC130067790:ATAC-STARR-seq lymphoblastoid silent region 13940 [Gene]
  • LOC130067791:ATAC-STARR-seq lymphoblastoid silent region 13941 [Gene]
  • LOC130067794:ATAC-STARR-seq lymphoblastoid silent region 13942 [Gene]
  • LOC130067797:ATAC-STARR-seq lymphoblastoid silent region 13943 [Gene]
  • LOC130067798:ATAC-STARR-seq lymphoblastoid silent region 13944 [Gene]
  • LOC130067802:ATAC-STARR-seq lymphoblastoid silent region 13945 [Gene]
  • LOC130067803:ATAC-STARR-seq lymphoblastoid silent region 13946 [Gene]
  • LOC130067805:ATAC-STARR-seq lymphoblastoid silent region 13947 [Gene]
  • LOC130067806:ATAC-STARR-seq lymphoblastoid silent region 13948 [Gene]
  • LOC130067808:ATAC-STARR-seq lymphoblastoid silent region 13949 [Gene]
  • LOC130067809:ATAC-STARR-seq lymphoblastoid silent region 13950 [Gene]
  • LOC130067810:ATAC-STARR-seq lymphoblastoid silent region 13951 [Gene]
  • LOC130067811:ATAC-STARR-seq lymphoblastoid silent region 13952 [Gene]
  • LOC130067812:ATAC-STARR-seq lymphoblastoid silent region 13953 [Gene]
  • LOC130067813:ATAC-STARR-seq lymphoblastoid silent region 13954 [Gene]
  • LOC130067819:ATAC-STARR-seq lymphoblastoid silent region 13955 [Gene]
  • LOC130067822:ATAC-STARR-seq lymphoblastoid silent region 13956 [Gene]
  • LOC130067823:ATAC-STARR-seq lymphoblastoid silent region 13957 [Gene]
  • LOC130067827:ATAC-STARR-seq lymphoblastoid silent region 13958 [Gene]
  • LOC130067828:ATAC-STARR-seq lymphoblastoid silent region 13959 [Gene]
  • LOC130067830:ATAC-STARR-seq lymphoblastoid silent region 13960 [Gene]
  • LOC130067831:ATAC-STARR-seq lymphoblastoid silent region 13961 [Gene]
  • LOC130067832:ATAC-STARR-seq lymphoblastoid silent region 13962 [Gene]
  • LOC130067833:ATAC-STARR-seq lymphoblastoid silent region 13963 [Gene]
  • LOC130067834:ATAC-STARR-seq lymphoblastoid silent region 13964 [Gene]
  • LOC130067835:ATAC-STARR-seq lymphoblastoid silent region 13965 [Gene]
  • LOC130067836:ATAC-STARR-seq lymphoblastoid silent region 13966 [Gene]
  • LOC130067837:ATAC-STARR-seq lymphoblastoid silent region 13968 [Gene]
  • LOC130067838:ATAC-STARR-seq lymphoblastoid silent region 13969 [Gene]
  • LOC130067840:ATAC-STARR-seq lymphoblastoid silent region 13970 [Gene]
  • LOC130067841:ATAC-STARR-seq lymphoblastoid silent region 13971 [Gene]
  • LOC130067842:ATAC-STARR-seq lymphoblastoid silent region 13972 [Gene]
  • LOC130067843:ATAC-STARR-seq lymphoblastoid silent region 13973 [Gene]
  • LOC130067844:ATAC-STARR-seq lymphoblastoid silent region 13974 [Gene]
  • LOC130067846:ATAC-STARR-seq lymphoblastoid silent region 13975 [Gene]
  • LOC130067849:ATAC-STARR-seq lymphoblastoid silent region 13976 [Gene]
  • LOC130067850:ATAC-STARR-seq lymphoblastoid silent region 13977 [Gene]
  • LOC130067851:ATAC-STARR-seq lymphoblastoid silent region 13978 [Gene]
  • LOC130067855:ATAC-STARR-seq lymphoblastoid silent region 13979 [Gene]
  • LOC130067856:ATAC-STARR-seq lymphoblastoid silent region 13981 [Gene]
  • LOC130067857:ATAC-STARR-seq lymphoblastoid silent region 13982 [Gene]
  • LOC130067859:ATAC-STARR-seq lymphoblastoid silent region 13983 [Gene]
  • LOC130067860:ATAC-STARR-seq lymphoblastoid silent region 13984 [Gene]
  • LOC130067861:ATAC-STARR-seq lymphoblastoid silent region 13985 [Gene]
  • LOC130067862:ATAC-STARR-seq lymphoblastoid silent region 13986 [Gene]
  • LOC130067865:ATAC-STARR-seq lymphoblastoid silent region 13987 [Gene]
  • LOC130067866:ATAC-STARR-seq lymphoblastoid silent region 13988 [Gene]
  • LOC130067867:ATAC-STARR-seq lymphoblastoid silent region 13989 [Gene]
  • LOC130067868:ATAC-STARR-seq lymphoblastoid silent region 13991 [Gene]
  • LOC130067869:ATAC-STARR-seq lymphoblastoid silent region 13992 [Gene]
  • LOC130067870:ATAC-STARR-seq lymphoblastoid silent region 13993 [Gene]
  • LOC130067871:ATAC-STARR-seq lymphoblastoid silent region 13994 [Gene]
  • LOC130067876:ATAC-STARR-seq lymphoblastoid silent region 13995 [Gene]
  • LOC130067877:ATAC-STARR-seq lymphoblastoid silent region 13996 [Gene]
  • LOC130067878:ATAC-STARR-seq lymphoblastoid silent region 13997 [Gene]
  • LOC130067880:ATAC-STARR-seq lymphoblastoid silent region 13998 [Gene]
  • LOC130067881:ATAC-STARR-seq lymphoblastoid silent region 13999 [Gene]
  • LOC130067882:ATAC-STARR-seq lymphoblastoid silent region 14000 [Gene]
  • LOC130067883:ATAC-STARR-seq lymphoblastoid silent region 14001 [Gene]
  • LOC130067884:ATAC-STARR-seq lymphoblastoid silent region 14002 [Gene]
  • LOC130067885:ATAC-STARR-seq lymphoblastoid silent region 14003 [Gene]
  • LOC130067887:ATAC-STARR-seq lymphoblastoid silent region 14004 [Gene]
  • LOC130067889:ATAC-STARR-seq lymphoblastoid silent region 14005 [Gene]
  • LOC126863179:BRD4-independent group 4 enhancer GRCh37_chr22:48279628-48280827 [Gene]
  • LOC126863180:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:48841523-48842722 [Gene]
  • LOC126863183:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:49678386-49679585 [Gene]
  • LOC126863187:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:51094338-51095537 [Gene]
  • LOC126863188:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:51142004-51143203 [Gene]
  • CHKB-DT:CHKB divergent transcript [Gene - HGNC]
  • CHKB-CPT1B:CHKB-CPT1B readthrough (NMD candidate) [Gene - HGNC]
  • DENND6B:DENN domain containing 6B [Gene - HGNC]
  • KLHDC7B-DT:KLHDC7B divergent transcript [Gene - HGNC]
  • LOC126863178:MED14-independent group 3 enhancer GRCh37_chr22:48268308-48269507 [Gene]
  • LOC126863181:MED14-independent group 3 enhancer GRCh37_chr22:49479476-49480675 [Gene]
  • LOC126863184:MED14-independent group 3 enhancer GRCh37_chr22:50720546-50721745 [Gene]
  • LOC126863186:MED14-independent group 3 enhancer GRCh37_chr22:50844619-50845818 [Gene]
  • MIR3667HG:MIR3667 host gene [Gene - HGNC]
  • LOC129391286:MPRA-validated peak4509 silencer [Gene]
  • LOC129391287:MPRA-validated peak4510 silencer [Gene]
  • LOC129391288:MPRA-validated peak4515 silencer [Gene]
  • LOC129391289:MPRA-validated peak4516 silencer [Gene]
  • LOC129391290:MPRA-validated peak4517 silencer [Gene]
  • LOC129391291:MPRA-validated peak4519 silencer [Gene]
  • MOV10L1:Mov10 like RNA helicase 1 [Gene - OMIM - HGNC]
  • LOC132090653:Neanderthal introgressed variant-containing enhancer experimental_63485 [Gene]
  • LOC132090654:Neanderthal introgressed variant-containing enhancer experimental_63487 [Gene]
  • LOC132090923:Neanderthal introgressed variant-containing enhancer experimental_63550 [Gene]
  • LOC132090655:Neanderthal introgressed variant-containing enhancer experimental_63573 [Gene]
  • LOC132090656:Neanderthal introgressed variant-containing enhancer experimental_63615 [Gene]
  • LOC132090924:Neanderthal introgressed variant-containing enhancer experimental_63621 [Gene]
  • LOC132090657:Neanderthal introgressed variant-containing enhancer experimental_63692 [Gene]
  • LOC108281149:ODF3B-KLHDC7B intergenic CAGE-defined mid-level expression enhancer [Gene]
  • LOC126863177:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:47983860-47985059 [Gene]
  • LOC126863182:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:49583849-49585048 [Gene]
  • LOC126863185:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:50743729-50744928 [Gene]
  • PIM3:Pim-3 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
  • RABL2B:RAB, member of RAS oncogene family like 2B [Gene - OMIM - HGNC]
  • SELENOO-AS1:SELENOO antisense RNA 1 [Gene - HGNC]
  • SBF1:SET binding factor 1 [Gene - OMIM - HGNC]
  • SHANK3:SH3 and multiple ankyrin repeat domains 3 [Gene - OMIM - HGNC]
  • LOC112695108:Sharpr-MPRA regulatory region 10948 [Gene]
  • LOC112695107:Sharpr-MPRA regulatory region 11110 [Gene]
  • LOC125446259:Sharpr-MPRA regulatory region 11654 [Gene]
  • LOC125446262:Sharpr-MPRA regulatory region 13947 [Gene]
  • LOC121853048:Sharpr-MPRA regulatory region 1531 [Gene]
  • LOC112695106:Sharpr-MPRA regulatory region 4711 [Gene]
  • LOC121627956:Sharpr-MPRA regulatory region 5053 [Gene]
  • LOC121853047:Sharpr-MPRA regulatory region 5393 [Gene]
  • LOC125446260:Sharpr-MPRA regulatory region 8073 [Gene]
  • LOC125446261:Sharpr-MPRA regulatory region 9327 [Gene]
  • LOC111828509:Sharpr-MPRA regulatory regions 3830 and 4902 [Gene]
  • TAFA5:TAFA chemokine like family member 5 [Gene - OMIM - HGNC]
  • TRABD-AS1:TRABD antisense RNA 1 [Gene - HGNC]
  • TRABD:TraB domain containing [Gene - HGNC]
  • ACR:acrosin [Gene - OMIM - HGNC]
  • ADM2:adrenomedullin 2 [Gene - OMIM - HGNC]
  • ARSA:arylsulfatase A [Gene - OMIM - HGNC]
  • BRD1:bromodomain containing 1 [Gene - OMIM - HGNC]
  • CPT1B:carnitine palmitoyltransferase 1B [Gene - OMIM - HGNC]
  • CHKB:choline kinase beta [Gene - OMIM - HGNC]
  • CIMAP1B:ciliary microtubule associated protein 1B [Gene - HGNC]
  • CRELD2:cysteine rich with EGF like domains 2 [Gene - OMIM - HGNC]
  • EPIC1:epigenetically induced MYC interacting lncRNA 1 [Gene - HGNC]
  • HDAC10:histone deacetylase 10 [Gene - OMIM - HGNC]
  • IL17REL:interleukin 17 receptor E like [Gene - OMIM - HGNC]
  • KLHDC7B:kelch domain containing 7B [Gene - OMIM - HGNC]
  • LMF2:lipase maturation factor 2 [Gene - HGNC]
  • LINC01310:long intergenic non-protein coding RNA 1310 [Gene - HGNC]
  • LINC00898:long intergenic non-protein coding RNA 898 [Gene - HGNC]
  • LOC107832855:meiotic recombination hotspot 22A [Gene]
  • MIR12114:microRNA 12114 [Gene - HGNC]
  • MIR3201:microRNA 3201 [Gene - HGNC]
  • MIR3667:microRNA 3667 [Gene - HGNC]
  • MIR4535:microRNA 4535 [Gene - HGNC]
  • MIR6821:microRNA 6821 [Gene - HGNC]
  • MAPK11:mitogen-activated protein kinase 11 [Gene - OMIM - HGNC]
  • MAPK12:mitogen-activated protein kinase 12 [Gene - OMIM - HGNC]
  • MAPK8IP2:mitogen-activated protein kinase 8 interacting protein 2 [Gene - OMIM - HGNC]
  • MLC1:modulator of VRAC current 1 [Gene - OMIM - HGNC]
  • MIOX:myo-inositol oxygenase [Gene - OMIM - HGNC]
  • NHIP:neuronal hypoxia inducible, placenta associated [Gene - HGNC]
  • NCAPH2:non-SMC condensin II complex subunit H2 [Gene - OMIM - HGNC]
  • PANX2:pannexin 2 [Gene - OMIM - HGNC]
  • PLXNB2:plexin B2 [Gene - OMIM - HGNC]
  • PPP6R2:protein phosphatase 6 regulatory subunit 2 [Gene - OMIM - HGNC]
  • SELENOO:selenoprotein O [Gene - OMIM - HGNC]
  • SYCE3:synaptonemal complex central element protein 3 [Gene - OMIM - HGNC]
  • SCO2:synthesis of cytochrome C oxidase 2 [Gene - OMIM - HGNC]
  • TYMP:thymidine phosphorylase [Gene - OMIM - HGNC]
  • TUBGCP6:tubulin gamma complex component 6 [Gene - OMIM - HGNC]
  • TTLL8:tubulin tyrosine ligase like 8 [Gene - OMIM - HGNC]
  • LOC105373100:uncharacterized LOC105373100 [Gene]
  • LOC105377205:uncharacterized LOC105377205 [Gene]
  • LOC284933:uncharacterized LOC284933 [Gene]
  • ZBED4:zinc finger BED-type containing 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
22q13.31-13.33
Genomic location:
Chr22: 47513236 - 50806138 (on Assembly GRCh38)
Preferred name:
NC_000022.11:g.47513236_50806138del
HGVS:
NC_000022.11:g.47513236_50806138del

Condition(s)

Name:
Phelan-McDermid syndrome
Synonyms:
TELOMERIC 22q13 MONOSOMY SYNDROME; 22q13.3 deletion syndrome; Chromosome 22q13.3 deletion syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011652; MedGen: C1853490; Orphanet: 48652; OMIM: 606232

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001430142Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
no assertion criteria provided
Pathogenicunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV001430142.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 14, 2023