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GRCh38/hg38 4p16.3(chr4:85149-1919505)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 12, 2011
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:
RCV000053259.4

Allele description [Variation Report for GRCh38/hg38 4p16.3(chr4:85149-1919505)x1]

GRCh38/hg38 4p16.3(chr4:85149-1919505)x1

Genes:
  • LOC129991944:ATAC-STARR-seq lymphoblastoid active region 21123 [Gene]
  • LOC129991945:ATAC-STARR-seq lymphoblastoid active region 21124 [Gene]
  • LOC129991946:ATAC-STARR-seq lymphoblastoid active region 21125 [Gene]
  • LOC129991949:ATAC-STARR-seq lymphoblastoid active region 21127 [Gene]
  • LOC129991951:ATAC-STARR-seq lymphoblastoid active region 21129 [Gene]
  • LOC129991954:ATAC-STARR-seq lymphoblastoid active region 21131 [Gene]
  • LOC129991955:ATAC-STARR-seq lymphoblastoid active region 21132 [Gene]
  • LOC129991957:ATAC-STARR-seq lymphoblastoid active region 21134 [Gene]
  • LOC129991959:ATAC-STARR-seq lymphoblastoid active region 21135 [Gene]
  • LOC129991960:ATAC-STARR-seq lymphoblastoid active region 21136 [Gene]
  • LOC129991961:ATAC-STARR-seq lymphoblastoid active region 21137 [Gene]
  • LOC129991964:ATAC-STARR-seq lymphoblastoid active region 21139 [Gene]
  • LOC129991966:ATAC-STARR-seq lymphoblastoid active region 21140 [Gene]
  • LOC129991969:ATAC-STARR-seq lymphoblastoid active region 21141 [Gene]
  • LOC129991970:ATAC-STARR-seq lymphoblastoid active region 21142 [Gene]
  • LOC129991976:ATAC-STARR-seq lymphoblastoid active region 21143 [Gene]
  • LOC129991977:ATAC-STARR-seq lymphoblastoid active region 21145 [Gene]
  • LOC129991978:ATAC-STARR-seq lymphoblastoid active region 21146 [Gene]
  • LOC129991979:ATAC-STARR-seq lymphoblastoid active region 21147 [Gene]
  • LOC129991980:ATAC-STARR-seq lymphoblastoid active region 21148 [Gene]
  • LOC129991982:ATAC-STARR-seq lymphoblastoid active region 21149 [Gene]
  • LOC129991985:ATAC-STARR-seq lymphoblastoid active region 21150 [Gene]
  • LOC129991986:ATAC-STARR-seq lymphoblastoid active region 21151 [Gene]
  • LOC129991987:ATAC-STARR-seq lymphoblastoid active region 21152 [Gene]
  • LOC129991993:ATAC-STARR-seq lymphoblastoid active region 21153 [Gene]
  • LOC129991997:ATAC-STARR-seq lymphoblastoid active region 21154 [Gene]
  • LOC129992002:ATAC-STARR-seq lymphoblastoid active region 21155 [Gene]
  • LOC129992003:ATAC-STARR-seq lymphoblastoid active region 21156 [Gene]
  • LOC129992004:ATAC-STARR-seq lymphoblastoid active region 21157 [Gene]
  • LOC129992005:ATAC-STARR-seq lymphoblastoid active region 21158 [Gene]
  • LOC129992006:ATAC-STARR-seq lymphoblastoid active region 21159 [Gene]
  • LOC129992007:ATAC-STARR-seq lymphoblastoid active region 21160 [Gene]
  • LOC129992013:ATAC-STARR-seq lymphoblastoid active region 21161 [Gene]
  • LOC129992017:ATAC-STARR-seq lymphoblastoid active region 21162 [Gene]
  • LOC129991947:ATAC-STARR-seq lymphoblastoid silent region 15096 [Gene]
  • LOC129991948:ATAC-STARR-seq lymphoblastoid silent region 15097 [Gene]
  • LOC129991950:ATAC-STARR-seq lymphoblastoid silent region 15098 [Gene]
  • LOC129991952:ATAC-STARR-seq lymphoblastoid silent region 15102 [Gene]
  • LOC129991953:ATAC-STARR-seq lymphoblastoid silent region 15103 [Gene]
  • LOC129991956:ATAC-STARR-seq lymphoblastoid silent region 15107 [Gene]
  • LOC129991958:ATAC-STARR-seq lymphoblastoid silent region 15110 [Gene]
  • LOC129991962:ATAC-STARR-seq lymphoblastoid silent region 15111 [Gene]
  • LOC129991963:ATAC-STARR-seq lymphoblastoid silent region 15112 [Gene]
  • LOC129991965:ATAC-STARR-seq lymphoblastoid silent region 15113 [Gene]
  • LOC129991967:ATAC-STARR-seq lymphoblastoid silent region 15114 [Gene]
  • LOC129991968:ATAC-STARR-seq lymphoblastoid silent region 15115 [Gene]
  • LOC129991971:ATAC-STARR-seq lymphoblastoid silent region 15117 [Gene]
  • LOC129991972:ATAC-STARR-seq lymphoblastoid silent region 15118 [Gene]
  • LOC129991973:ATAC-STARR-seq lymphoblastoid silent region 15120 [Gene]
  • LOC129991974:ATAC-STARR-seq lymphoblastoid silent region 15121 [Gene]
  • LOC129991975:ATAC-STARR-seq lymphoblastoid silent region 15122 [Gene]
  • LOC129991981:ATAC-STARR-seq lymphoblastoid silent region 15123 [Gene]
  • LOC129991983:ATAC-STARR-seq lymphoblastoid silent region 15124 [Gene]
  • LOC129991984:ATAC-STARR-seq lymphoblastoid silent region 15125 [Gene]
  • LOC129991988:ATAC-STARR-seq lymphoblastoid silent region 15126 [Gene]
  • LOC129991989:ATAC-STARR-seq lymphoblastoid silent region 15127 [Gene]
  • LOC129991990:ATAC-STARR-seq lymphoblastoid silent region 15128 [Gene]
  • LOC129991991:ATAC-STARR-seq lymphoblastoid silent region 15129 [Gene]
  • LOC129991992:ATAC-STARR-seq lymphoblastoid silent region 15130 [Gene]
  • LOC129991994:ATAC-STARR-seq lymphoblastoid silent region 15132 [Gene]
  • LOC129991995:ATAC-STARR-seq lymphoblastoid silent region 15133 [Gene]
  • LOC129991996:ATAC-STARR-seq lymphoblastoid silent region 15134 [Gene]
  • LOC129991998:ATAC-STARR-seq lymphoblastoid silent region 15136 [Gene]
  • LOC129991999:ATAC-STARR-seq lymphoblastoid silent region 15137 [Gene]
  • LOC129992000:ATAC-STARR-seq lymphoblastoid silent region 15138 [Gene]
  • LOC129992001:ATAC-STARR-seq lymphoblastoid silent region 15139 [Gene]
  • LOC129992008:ATAC-STARR-seq lymphoblastoid silent region 15140 [Gene]
  • LOC129992009:ATAC-STARR-seq lymphoblastoid silent region 15142 [Gene]
  • LOC129992010:ATAC-STARR-seq lymphoblastoid silent region 15143 [Gene]
  • LOC129992011:ATAC-STARR-seq lymphoblastoid silent region 15144 [Gene]
  • LOC129992012:ATAC-STARR-seq lymphoblastoid silent region 15145 [Gene]
  • LOC129992014:ATAC-STARR-seq lymphoblastoid silent region 15148 [Gene]
  • LOC129992015:ATAC-STARR-seq lymphoblastoid silent region 15150 [Gene]
  • LOC129992016:ATAC-STARR-seq lymphoblastoid silent region 15151 [Gene]
  • ATP5ME:ATP synthase membrane subunit e [Gene - OMIM - HGNC]
  • LOC126806942:BRD4-independent group 4 enhancer GRCh37_chr4:1190349-1191548 [Gene]
  • LOC126806943:BRD4-independent group 4 enhancer GRCh37_chr4:1317288-1318487 [Gene]
  • LOC126806939:BRD4-independent group 4 enhancer GRCh37_chr4:581897-583096 [Gene]
  • CTBP1:C-terminal binding protein 1 [Gene - OMIM - HGNC]
  • LOC126806944:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:1319662-1320861 [Gene]
  • LOC126806940:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:860125-861324 [Gene]
  • LOC126806941:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:872957-874156 [Gene]
  • LOC116158483:CRISPRi-validated cis-regulatory element chr4.260 [Gene]
  • CTBP1-AS:CTBP1 antisense RNA [Gene - HGNC]
  • CTBP1-DT:CTBP1 divergent transcript [Gene - HGNC]
  • NKX1-1:NK1 homeobox 1 [Gene - OMIM - HGNC]
  • LOC126806945:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:1388225-1389424 [Gene]
  • PCGF3-AS1:PCGF3 antisense RNA 1 [Gene - HGNC]
  • PDE6B-AS1:PDE6B antisense RNA 1 [Gene - HGNC]
  • LOC114004383:Sharpr-MPRA regulatory region 3424 [Gene]
  • LOC114004382:Sharpr-MPRA regulatory region 8056 [Gene]
  • UVSSA:UV stimulated scaffold protein A [Gene - OMIM - HGNC]
  • LOC110120693:VISTA enhancer hs526 [Gene]
  • IDUA:alpha-L-iduronidase [Gene - OMIM - HGNC]
  • CPLX1:complexin 1 [Gene - OMIM - HGNC]
  • GAK:cyclin G associated kinase [Gene - OMIM - HGNC]
  • CRIPAK:cysteine rich PAK1 inhibitor [Gene - OMIM - HGNC]
  • DGKQ:diacylglycerol kinase theta [Gene - OMIM - HGNC]
  • FAM53A:family with sequence similarity 53 member A [Gene - OMIM - HGNC]
  • FGFR3:fibroblast growth factor receptor 3 [Gene - OMIM - HGNC]
  • FGFRL1:fibroblast growth factor receptor like 1 [Gene - OMIM - HGNC]
  • LETM1:leucine zipper and EF-hand containing transmembrane protein 1 [Gene - OMIM - HGNC]
  • MAEA:macrophage erythroblast attacher, E3 ubiquitin ligase [Gene - OMIM - HGNC]
  • MIR571:microRNA 571 [Gene - HGNC]
  • MYL5:myosin light chain 5 [Gene - OMIM - HGNC]
  • NSD2:nuclear receptor binding SET domain protein 2 [Gene - OMIM - HGNC]
  • PIGG:phosphatidylinositol glycan anchor biosynthesis class G [Gene - OMIM - HGNC]
  • PDE6B:phosphodiesterase 6B [Gene - OMIM - HGNC]
  • PCGF3:polycomb group ring finger 3 [Gene - OMIM - HGNC]
  • RNF212:ring finger protein 212 [Gene - OMIM - HGNC]
  • SLC26A1:solute carrier family 26 member 1 [Gene - OMIM - HGNC]
  • SLC49A3:solute carrier family 49 member 3 [Gene - OMIM - HGNC]
  • SPON2:spondin 2 [Gene - OMIM - HGNC]
  • SLBP:stem-loop histone mRNA binding protein [Gene - OMIM - HGNC]
  • TACC3:transforming acidic coiled-coil containing protein 3 [Gene - OMIM - HGNC]
  • TMEM129:transmembrane protein 129, E3 ubiquitin ligase [Gene - OMIM - HGNC]
  • TMEM175:transmembrane protein 175 [Gene - OMIM - HGNC]
  • TMEM271:transmembrane protein 271 [Gene - HGNC]
  • LOC100130872:uncharacterized LOC100130872 [Gene]
  • LOC105374338:uncharacterized LOC105374338 [Gene]
  • LOC105374344:uncharacterized LOC105374344 [Gene]
  • ZNF141:zinc finger protein 141 [Gene - OMIM - HGNC]
  • ZNF595:zinc finger protein 595 [Gene - HGNC]
  • ZNF718:zinc finger protein 718 [Gene - HGNC]
  • ZNF721:zinc finger protein 721 [Gene - HGNC]
  • ZNF732:zinc finger protein 732 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
GRCh38/hg38 4p16.3(chr4:85149-1919505)x1
HGVS:
  • NC_000004.12:g.(?_85149)_(1919505_?)del
  • NC_000004.10:g.(?_75040)_(1891030_?)del
  • NC_000004.11:g.(?_85040)_(1921232_?)del
Links:
dbVar: nssv577963; dbVar: nsv531939
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
SCV000080617GeneDx
criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		not providedclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, et al.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

PubMed [citation]
PMID:
21844811
PMCID:
PMC3661946

Details of each submission

From GeneDx, SCV000080617.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providedyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: Oct 14, 2023