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Single allele AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 24, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002247742.2

Allele description [Variation Report for Single allele]

Genes:
  • LOC130068821:ATAC-STARR-seq lymphoblastoid active region 30033 [Gene]
  • LOC130068822:ATAC-STARR-seq lymphoblastoid active region 30034 [Gene]
  • LOC130068823:ATAC-STARR-seq lymphoblastoid active region 30035 [Gene]
  • LOC130068824:ATAC-STARR-seq lymphoblastoid active region 30036 [Gene]
  • LOC130068832:ATAC-STARR-seq lymphoblastoid active region 30037 [Gene]
  • LOC130068833:ATAC-STARR-seq lymphoblastoid active region 30038 [Gene]
  • LOC130068834:ATAC-STARR-seq lymphoblastoid active region 30039 [Gene]
  • LOC130068836:ATAC-STARR-seq lymphoblastoid active region 30041 [Gene]
  • LOC130068837:ATAC-STARR-seq lymphoblastoid active region 30042 [Gene]
  • LOC130068841:ATAC-STARR-seq lymphoblastoid active region 30043 [Gene]
  • LOC130068842:ATAC-STARR-seq lymphoblastoid active region 30044 [Gene]
  • LOC130068843:ATAC-STARR-seq lymphoblastoid active region 30045 [Gene]
  • LOC130068847:ATAC-STARR-seq lymphoblastoid active region 30047 [Gene]
  • LOC130068848:ATAC-STARR-seq lymphoblastoid active region 30048 [Gene]
  • LOC130068851:ATAC-STARR-seq lymphoblastoid active region 30052 [Gene]
  • LOC130068852:ATAC-STARR-seq lymphoblastoid active region 30053 [Gene]
  • LOC130068855:ATAC-STARR-seq lymphoblastoid active region 30055 [Gene]
  • LOC129929050:ATAC-STARR-seq lymphoblastoid active region 30056 [Gene]
  • LOC129929051:ATAC-STARR-seq lymphoblastoid active region 30057 [Gene]
  • LOC130068859:ATAC-STARR-seq lymphoblastoid active region 30059 [Gene]
  • LOC130068867:ATAC-STARR-seq lymphoblastoid active region 30060 [Gene]
  • LOC130068868:ATAC-STARR-seq lymphoblastoid active region 30061 [Gene]
  • LOC130068872:ATAC-STARR-seq lymphoblastoid active region 30062 [Gene]
  • LOC130068877:ATAC-STARR-seq lymphoblastoid active region 30063 [Gene]
  • LOC130068878:ATAC-STARR-seq lymphoblastoid active region 30064 [Gene]
  • LOC130068880:ATAC-STARR-seq lymphoblastoid active region 30065 [Gene]
  • LOC130068881:ATAC-STARR-seq lymphoblastoid active region 30067 [Gene]
  • LOC130068885:ATAC-STARR-seq lymphoblastoid active region 30068 [Gene]
  • LOC130068887:ATAC-STARR-seq lymphoblastoid active region 30069 [Gene]
  • LOC130068889:ATAC-STARR-seq lymphoblastoid active region 30070 [Gene]
  • LOC130068890:ATAC-STARR-seq lymphoblastoid active region 30071 [Gene]
  • LOC130068891:ATAC-STARR-seq lymphoblastoid active region 30072 [Gene]
  • LOC130068892:ATAC-STARR-seq lymphoblastoid active region 30073 [Gene]
  • LOC130068895:ATAC-STARR-seq lymphoblastoid active region 30074 [Gene]
  • LOC130068898:ATAC-STARR-seq lymphoblastoid active region 30078 [Gene]
  • LOC130068825:ATAC-STARR-seq lymphoblastoid silent region 21064 [Gene]
  • LOC130068826:ATAC-STARR-seq lymphoblastoid silent region 21065 [Gene]
  • LOC130068827:ATAC-STARR-seq lymphoblastoid silent region 21066 [Gene]
  • LOC130068828:ATAC-STARR-seq lymphoblastoid silent region 21067 [Gene]
  • LOC130068829:ATAC-STARR-seq lymphoblastoid silent region 21068 [Gene]
  • LOC130068830:ATAC-STARR-seq lymphoblastoid silent region 21069 [Gene]
  • LOC130068831:ATAC-STARR-seq lymphoblastoid silent region 21070 [Gene]
  • LOC130068835:ATAC-STARR-seq lymphoblastoid silent region 21072 [Gene]
  • LOC130068838:ATAC-STARR-seq lymphoblastoid silent region 21073 [Gene]
  • LOC130068839:ATAC-STARR-seq lymphoblastoid silent region 21074 [Gene]
  • LOC130068840:ATAC-STARR-seq lymphoblastoid silent region 21075 [Gene]
  • LOC130068844:ATAC-STARR-seq lymphoblastoid silent region 21077 [Gene]
  • LOC130068845:ATAC-STARR-seq lymphoblastoid silent region 21078 [Gene]
  • LOC130068846:ATAC-STARR-seq lymphoblastoid silent region 21079 [Gene]
  • LOC130068849:ATAC-STARR-seq lymphoblastoid silent region 21080 [Gene]
  • LOC130068850:ATAC-STARR-seq lymphoblastoid silent region 21081 [Gene]
  • LOC130068853:ATAC-STARR-seq lymphoblastoid silent region 21083 [Gene]
  • LOC130068854:ATAC-STARR-seq lymphoblastoid silent region 21085 [Gene]
  • LOC130068856:ATAC-STARR-seq lymphoblastoid silent region 21086 [Gene]
  • LOC130068857:ATAC-STARR-seq lymphoblastoid silent region 21087 [Gene]
  • LOC130068858:ATAC-STARR-seq lymphoblastoid silent region 21093 [Gene]
  • LOC130068860:ATAC-STARR-seq lymphoblastoid silent region 21094 [Gene]
  • LOC130068861:ATAC-STARR-seq lymphoblastoid silent region 21095 [Gene]
  • LOC130068862:ATAC-STARR-seq lymphoblastoid silent region 21096 [Gene]
  • LOC130068863:ATAC-STARR-seq lymphoblastoid silent region 21097 [Gene]
  • LOC130068864:ATAC-STARR-seq lymphoblastoid silent region 21098 [Gene]
  • LOC130068865:ATAC-STARR-seq lymphoblastoid silent region 21099 [Gene]
  • LOC130068866:ATAC-STARR-seq lymphoblastoid silent region 21100 [Gene]
  • LOC130068869:ATAC-STARR-seq lymphoblastoid silent region 21101 [Gene]
  • LOC130068870:ATAC-STARR-seq lymphoblastoid silent region 21104 [Gene]
  • LOC130068871:ATAC-STARR-seq lymphoblastoid silent region 21105 [Gene]
  • LOC130068873:ATAC-STARR-seq lymphoblastoid silent region 21106 [Gene]
  • LOC130068874:ATAC-STARR-seq lymphoblastoid silent region 21107 [Gene]
  • LOC130068875:ATAC-STARR-seq lymphoblastoid silent region 21108 [Gene]
  • LOC130068876:ATAC-STARR-seq lymphoblastoid silent region 21109 [Gene]
  • LOC130068879:ATAC-STARR-seq lymphoblastoid silent region 21112 [Gene]
  • LOC129929052:ATAC-STARR-seq lymphoblastoid silent region 21114 [Gene]
  • LOC130068882:ATAC-STARR-seq lymphoblastoid silent region 21115 [Gene]
  • LOC130068883:ATAC-STARR-seq lymphoblastoid silent region 21116 [Gene]
  • LOC130068884:ATAC-STARR-seq lymphoblastoid silent region 21117 [Gene]
  • LOC130068886:ATAC-STARR-seq lymphoblastoid silent region 21118 [Gene]
  • LOC130068888:ATAC-STARR-seq lymphoblastoid silent region 21119 [Gene]
  • LOC130068893:ATAC-STARR-seq lymphoblastoid silent region 21120 [Gene]
  • LOC130068894:ATAC-STARR-seq lymphoblastoid silent region 21121 [Gene]
  • LOC130068896:ATAC-STARR-seq lymphoblastoid silent region 21124 [Gene]
  • LOC130068897:ATAC-STARR-seq lymphoblastoid silent region 21125 [Gene]
  • ABCD1:ATP binding cassette subfamily D member 1 [Gene - OMIM - HGNC]
  • ATP6AP1-DT:ATP6AP1 divergent transcript [Gene - HGNC]
  • ATP6AP1:ATPase H+ transporting accessory protein 1 [Gene - OMIM - HGNC]
  • ATP2B3:ATPase plasma membrane Ca2+ transporting 3 [Gene - OMIM - HGNC]
  • BCAP31:B cell receptor associated protein 31 [Gene - OMIM - HGNC]
  • BRCC3:BRCA1/BRCA2-containing complex subunit 3 [Gene - OMIM - HGNC]
  • CMC4:C-X9-C motif containing 4 [Gene - OMIM - HGNC]
  • LOC116309161:CRISPRi-validated cis-regulatory element chrX.2654 [Gene]
  • LOC116309162:CRISPRi-validated cis-regulatory element chrX.2695 [Gene]
  • FAM3A:FAM3 metabolism regulating signaling molecule A [Gene - OMIM - HGNC]
  • FUNDC2:FUN14 domain containing 2 [Gene - OMIM - HGNC]
  • LOC108281126:G6PD and IKBKG intron CAGE-defined low expression enhancer [Gene]
  • GDI1:GDP dissociation inhibitor 1 [Gene - OMIM - HGNC]
  • GAB3:GRB2 associated binding protein 3 [Gene - OMIM - HGNC]
  • H2AB1:H2A.B variant histone 1 [Gene - OMIM - HGNC]
  • H2AB2:H2A.B variant histone 2 [Gene - OMIM - HGNC]
  • H2AB3:H2A.B variant histone 3 [Gene - OMIM - HGNC]
  • HAUS7:HAUS augmin like complex subunit 7 [Gene - OMIM - HGNC]
  • HCFC1-AS1:HCFC1 antisense RNA 1 [Gene - HGNC]
  • LOC111589209:HNF4 motif-containing MPRA enhancer 232 [Gene]
  • LOC107988022:IKBKG downstream recombination region [Gene]
  • LOC107988021:IKBKG recombination region [Gene]
  • LOC107988024:IKBKGP1 recombination region [Gene]
  • LOC107988025:IKBKGP1 upstream recombination region [Gene]
  • LAGE3:L antigen family member 3 [Gene - OMIM - HGNC]
  • L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]
  • L1CAM-AS1:L1CAM antisense RNA 1 [Gene - HGNC]
  • MPP1:MAGUK p55 scaffold protein 1 [Gene - OMIM - HGNC]
  • NAA10:N-alpha-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
  • LOC111365170:NFE2L2 motif-containing MPRA enhancer 190/191 [Gene]
  • LOC126863349:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:154195537-154196736 [Gene]
  • PDZD4:PDZ domain containing 4 [Gene - OMIM - HGNC]
  • PLXNB3-AS1:PLXNB3 antisense RNA 1 [Gene - HGNC]
  • RAB39B:RAB39B, member RAS oncogene family [Gene - OMIM - HGNC]
  • ARHGAP4:Rho GTPase activating protein 4 [Gene - OMIM - HGNC]
  • SRPK3:SRSF protein kinase 3 [Gene - OMIM - HGNC]
  • LOC121627985:Sharpr-MPRA regulatory region 11639 [Gene]
  • LOC113875015:Sharpr-MPRA regulatory region 12525 [Gene]
  • LOC125467794:Sharpr-MPRA regulatory region 13577 [Gene]
  • LOC121853072:Sharpr-MPRA regulatory region 3405 [Gene]
  • LOC121627986:Sharpr-MPRA regulatory region 3530 [Gene]
  • LOC125467793:Sharpr-MPRA regulatory region 3572 [Gene]
  • LOC125467795:Sharpr-MPRA regulatory region 4209 [Gene]
  • LOC121853071:Sharpr-MPRA regulatory region 5891 [Gene]
  • LOC113875016:Sharpr-MPRA regulatory region 7862 [Gene]
  • LOC113875014:Sharpr-MPRA regulatory region 9358 [Gene]
  • TMLHE-AS1:TMLHE antisense RNA 1 [Gene - HGNC]
  • VBP1:VHL binding protein 1 [Gene - OMIM - HGNC]
  • LOC107988033:Xq28 distal FLNA-EMD recombination region [Gene]
  • LOC107988032:Xq28 proximal FLNA-EMD recombination region [Gene]
  • AVPR2:arginine vasopressin receptor 2 [Gene - OMIM - HGNC]
  • BGN:biglycan [Gene - OMIM - HGNC]
  • CTAG1A:cancer/testis antigen 1A [Gene - OMIM - HGNC]
  • CTAG1B:cancer/testis antigen 1B [Gene - OMIM - HGNC]
  • CTAG2:cancer/testis antigen 2 [Gene - OMIM - HGNC]
  • CLIC2:chloride intracellular channel 2 [Gene - OMIM - HGNC]
  • F8A1:coagulation factor VIII associated 1 [Gene - OMIM - HGNC]
  • F8A2:coagulation factor VIII associated 2 [Gene - HGNC]
  • F8A3:coagulation factor VIII associated 3 [Gene - HGNC]
  • F8:coagulation factor VIII [Gene - OMIM - HGNC]
  • CCNQ:cyclin Q [Gene - OMIM - HGNC]
  • DNASE1L1:deoxyribonuclease 1 like 1 [Gene - OMIM - HGNC]
  • DUSP9:dual specificity phosphatase 9 [Gene - OMIM - HGNC]
  • DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]
  • EMD:emerin [Gene - OMIM - HGNC]
  • FAM223A:family with sequence similarity 223 member A [Gene - HGNC]
  • FAM223B:family with sequence similarity 223 member B [Gene - HGNC]
  • FAM50A:family with sequence similarity 50 member A [Gene - OMIM - HGNC]
  • FLNA:filamin A [Gene - OMIM - HGNC]
  • G6PD:glucose-6-phosphate dehydrogenase [Gene - OMIM - HGNC]
  • HCFC1:host cell factor C1 [Gene - OMIM - HGNC]
  • IKBKG:inhibitor of nuclear factor kappa B kinase regulatory subunit gamma [Gene - OMIM - HGNC]
  • LOC106146143:int1h-1 recombination region [Gene]
  • LOC106146144:int1h-2 recombination region [Gene]
  • LOC106146150:int22h-1 recombination region [Gene]
  • LOC106146151:int22h-2 recombination region [Gene]
  • LOC106146152:int22h-3 recombination region [Gene]
  • IRAK1:interleukin 1 receptor associated kinase 1 [Gene - OMIM - HGNC]
  • IL9R:interleukin 9 receptor [Gene - OMIM - HGNC]
  • IDH3G:isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [Gene - OMIM - HGNC]
  • MTCP1:mature T cell proliferation 1 [Gene - OMIM - HGNC]
  • LOC107522039:meiotic recombination hotspot PAR2 [Gene]
  • LOC107838685:meiotic recombination hotspot PAR2A [Gene]
  • MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
  • MIR1184-1:microRNA 1184-1 [Gene - HGNC]
  • MIR1184-2:microRNA 1184-2 [Gene - HGNC]
  • MIR1184-3:microRNA 1184-3 [Gene - HGNC]
  • MIR3202-1:microRNA 3202-1 [Gene - HGNC]
  • MIR3202-2:microRNA 3202-2 [Gene - HGNC]
  • MIR664B:microRNA 664b [Gene - HGNC]
  • MIR6858:microRNA 6858 [Gene - HGNC]
  • MIR718:microRNA 718 [Gene - OMIM - HGNC]
  • OPN1LW:opsin 1, long wave sensitive [Gene - OMIM - HGNC]
  • OPN1MW2:opsin 1, medium wave sensitive 2 [Gene - HGNC]
  • OPN1MW3:opsin 1, medium wave sensitive 3 [Gene - HGNC]
  • OPN1MW:opsin 1, medium wave sensitive [Gene - OMIM - HGNC]
  • OPSIN-LCR:opsin locus control region [Gene - OMIM]
  • LOC107181288:origin of replication in promoter of G6PD [Gene]
  • PLXNA3:plexin A3 [Gene - OMIM - HGNC]
  • PLXNB3:plexin B3 [Gene - OMIM - HGNC]
  • PNCK:pregnancy up-regulated nonubiquitous CaM kinase [Gene - OMIM - HGNC]
  • RENBP:renin binding protein [Gene - OMIM - HGNC]
  • RPL10:ribosomal protein L10 [Gene - OMIM - HGNC]
  • SSR4:signal sequence receptor subunit 4 [Gene - OMIM - HGNC]
  • SMIM9:small integral membrane protein 9 [Gene - HGNC]
  • SNORA36A:small nucleolar RNA, H/ACA box 36A [Gene - HGNC]
  • SNORA56:small nucleolar RNA, H/ACA box 56 [Gene - HGNC]
  • SNORA70:small nucleolar RNA, H/ACA box 70 [Gene - HGNC]
  • SLC10A3:solute carrier family 10 member 3 [Gene - OMIM - HGNC]
  • SLC6A8:solute carrier family 6 member 8 [Gene - OMIM - HGNC]
  • SPRY3:sprouty RTK signaling antagonist 3 [Gene - OMIM - HGNC]
  • TAFAZZIN:tafazzin, phospholipid-lysophospholipid transacylase [Gene - OMIM - HGNC]
  • TEX28:testis expressed 28 [Gene - OMIM - HGNC]
  • TREX2:three prime repair exonuclease 2 [Gene - OMIM - HGNC]
  • TKTL1:transketolase like 1 [Gene - OMIM - HGNC]
  • TMEM187:transmembrane protein 187 [Gene - OMIM - HGNC]
  • TMLHE:trimethyllysine hydroxylase, epsilon [Gene - OMIM - HGNC]
  • UBL4A:ubiquitin like 4A [Gene - OMIM - HGNC]
  • LOC101927830:uncharacterized LOC101927830 [Gene]
  • LOC105373383:uncharacterized LOC105373383 [Gene]
  • VAMP7:vesicle associated membrane protein 7 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xq28
Genomic location:
ChrX: 153427468 - 156004919 (on Assembly GRCh38)
Other names:
del(X)(q28q28)

Condition(s)

Name:
Immunodeficiency 33 (IMD33)
Synonyms:
Immunodeficiency without anhidrotic ectodermal dysplasia; X-linked mendelian susceptibility to mycobacterial diseases due to IKBKG deficiency
Identifiers:
MONDO: MONDO:0010386; MedGen: C1970879; Orphanet: 319605; Orphanet: 319612; OMIM: 300636
Name:
Ectodermal dysplasia and immunodeficiency 1 (EDAID1)
Synonyms:
Ectodermal dysplasia, anhidrotic, with immunodeficiency, osteopetrosis, and lymphedema; ECTODERMAL DYSPLASIA AND IMMUNE DEFICIENCY 1; Hyper-IgM immunodeficiency, X-linked, with hypohidrotic ectodermal dysplasia; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0020740; MedGen: C1846008; Orphanet: 238468; Orphanet: 98813; OMIM: 300291
Name:
Incontinentia pigmenti syndrome (IP)
Synonyms:
INCONTINENTIA PIGMENTI, TYPE II; Incontinentia pigmenti, familial male-lethal type; Bloch-Sulzberger syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010631; MedGen: C0021171; Orphanet: 464; OMIM: 308300
Name:
Immunodeficiency 47 (IMD47)
Synonyms:
IMMUNODEFICIENCY AND HEPATOPATHY WITH OR WITHOUT NEUROLOGIC FEATURES
Identifiers:
MONDO: MONDO:0010504; MedGen: C4310819; OMIM: 300972

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002516003Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Feb 24, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV002516003.1

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

Last Updated: Jun 17, 2024