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GRCh38/hg38 4p16.3(chr4:620566-2958209)x3 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:
RCV000050834.5

Allele description [Variation Report for GRCh38/hg38 4p16.3(chr4:620566-2958209)x3]

GRCh38/hg38 4p16.3(chr4:620566-2958209)x3

Genes:
  • 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]
  • LOC129992022:ATAC-STARR-seq lymphoblastoid active region 21164 [Gene]
  • LOC129992029:ATAC-STARR-seq lymphoblastoid active region 21166 [Gene]
  • LOC129992033:ATAC-STARR-seq lymphoblastoid active region 21170 [Gene]
  • LOC129992034:ATAC-STARR-seq lymphoblastoid active region 21171 [Gene]
  • LOC129992035:ATAC-STARR-seq lymphoblastoid active region 21172 [Gene]
  • LOC129992036:ATAC-STARR-seq lymphoblastoid active region 21173 [Gene]
  • LOC129992042:ATAC-STARR-seq lymphoblastoid active region 21175 [Gene]
  • LOC129992043:ATAC-STARR-seq lymphoblastoid active region 21176 [Gene]
  • LOC129992044:ATAC-STARR-seq lymphoblastoid active region 21177 [Gene]
  • LOC129992051:ATAC-STARR-seq lymphoblastoid active region 21178 [Gene]
  • LOC129992052:ATAC-STARR-seq lymphoblastoid active region 21179 [Gene]
  • LOC129992053:ATAC-STARR-seq lymphoblastoid active region 21180 [Gene]
  • LOC129992054:ATAC-STARR-seq lymphoblastoid active region 21181 [Gene]
  • LOC129992055:ATAC-STARR-seq lymphoblastoid active region 21182 [Gene]
  • LOC129992060:ATAC-STARR-seq lymphoblastoid active region 21183 [Gene]
  • LOC129992061:ATAC-STARR-seq lymphoblastoid active region 21184 [Gene]
  • LOC129992062:ATAC-STARR-seq lymphoblastoid active region 21185 [Gene]
  • LOC129992063:ATAC-STARR-seq lymphoblastoid active region 21186 [Gene]
  • LOC129992065:ATAC-STARR-seq lymphoblastoid active region 21188 [Gene]
  • LOC129992066:ATAC-STARR-seq lymphoblastoid active region 21189 [Gene]
  • LOC129992067:ATAC-STARR-seq lymphoblastoid active region 21191 [Gene]
  • LOC129992072:ATAC-STARR-seq lymphoblastoid active region 21192 [Gene]
  • LOC129992073:ATAC-STARR-seq lymphoblastoid active region 21193 [Gene]
  • LOC129992074:ATAC-STARR-seq lymphoblastoid active region 21194 [Gene]
  • LOC129992079:ATAC-STARR-seq lymphoblastoid active region 21195 [Gene]
  • LOC129992080:ATAC-STARR-seq lymphoblastoid active region 21196 [Gene]
  • LOC129992082:ATAC-STARR-seq lymphoblastoid active region 21197 [Gene]
  • LOC129992083:ATAC-STARR-seq lymphoblastoid active region 21198 [Gene]
  • LOC129992084:ATAC-STARR-seq lymphoblastoid active region 21199 [Gene]
  • LOC129992085:ATAC-STARR-seq lymphoblastoid active region 21200 [Gene]
  • LOC129992086:ATAC-STARR-seq lymphoblastoid active region 21201 [Gene]
  • LOC129992087:ATAC-STARR-seq lymphoblastoid active region 21202 [Gene]
  • LOC129992090:ATAC-STARR-seq lymphoblastoid active region 21204 [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]
  • LOC129992018:ATAC-STARR-seq lymphoblastoid silent region 15152 [Gene]
  • LOC129992019:ATAC-STARR-seq lymphoblastoid silent region 15153 [Gene]
  • LOC129992020:ATAC-STARR-seq lymphoblastoid silent region 15154 [Gene]
  • LOC129992021:ATAC-STARR-seq lymphoblastoid silent region 15155 [Gene]
  • LOC129992023:ATAC-STARR-seq lymphoblastoid silent region 15156 [Gene]
  • LOC129992024:ATAC-STARR-seq lymphoblastoid silent region 15157 [Gene]
  • LOC129992025:ATAC-STARR-seq lymphoblastoid silent region 15158 [Gene]
  • LOC129992026:ATAC-STARR-seq lymphoblastoid silent region 15159 [Gene]
  • LOC129992027:ATAC-STARR-seq lymphoblastoid silent region 15160 [Gene]
  • LOC129992028:ATAC-STARR-seq lymphoblastoid silent region 15161 [Gene]
  • LOC129992030:ATAC-STARR-seq lymphoblastoid silent region 15163 [Gene]
  • LOC129992031:ATAC-STARR-seq lymphoblastoid silent region 15164 [Gene]
  • LOC129992032:ATAC-STARR-seq lymphoblastoid silent region 15165 [Gene]
  • LOC129992037:ATAC-STARR-seq lymphoblastoid silent region 15166 [Gene]
  • LOC129992038:ATAC-STARR-seq lymphoblastoid silent region 15167 [Gene]
  • LOC129992039:ATAC-STARR-seq lymphoblastoid silent region 15168 [Gene]
  • LOC129992040:ATAC-STARR-seq lymphoblastoid silent region 15169 [Gene]
  • LOC129992041:ATAC-STARR-seq lymphoblastoid silent region 15170 [Gene]
  • LOC129992045:ATAC-STARR-seq lymphoblastoid silent region 15171 [Gene]
  • LOC129992046:ATAC-STARR-seq lymphoblastoid silent region 15172 [Gene]
  • LOC129992047:ATAC-STARR-seq lymphoblastoid silent region 15173 [Gene]
  • LOC129992048:ATAC-STARR-seq lymphoblastoid silent region 15174 [Gene]
  • LOC129992049:ATAC-STARR-seq lymphoblastoid silent region 15175 [Gene]
  • LOC129992050:ATAC-STARR-seq lymphoblastoid silent region 15176 [Gene]
  • LOC129992056:ATAC-STARR-seq lymphoblastoid silent region 15178 [Gene]
  • LOC129992057:ATAC-STARR-seq lymphoblastoid silent region 15179 [Gene]
  • LOC129992058:ATAC-STARR-seq lymphoblastoid silent region 15180 [Gene]
  • LOC129992059:ATAC-STARR-seq lymphoblastoid silent region 15181 [Gene]
  • LOC129992064:ATAC-STARR-seq lymphoblastoid silent region 15182 [Gene]
  • LOC129992068:ATAC-STARR-seq lymphoblastoid silent region 15183 [Gene]
  • LOC129992069:ATAC-STARR-seq lymphoblastoid silent region 15184 [Gene]
  • LOC129992070:ATAC-STARR-seq lymphoblastoid silent region 15185 [Gene]
  • LOC129992071:ATAC-STARR-seq lymphoblastoid silent region 15186 [Gene]
  • LOC129992075:ATAC-STARR-seq lymphoblastoid silent region 15187 [Gene]
  • LOC129992076:ATAC-STARR-seq lymphoblastoid silent region 15188 [Gene]
  • LOC129992077:ATAC-STARR-seq lymphoblastoid silent region 15189 [Gene]
  • LOC129992078:ATAC-STARR-seq lymphoblastoid silent region 15190 [Gene]
  • LOC129992081:ATAC-STARR-seq lymphoblastoid silent region 15191 [Gene]
  • LOC129992088:ATAC-STARR-seq lymphoblastoid silent region 15193 [Gene]
  • LOC129992089:ATAC-STARR-seq lymphoblastoid silent region 15194 [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]
  • LOC126806946:BRD4-independent group 4 enhancer GRCh37_chr4:2175172-2176371 [Gene]
  • LOC126806948:BRD4-independent group 4 enhancer GRCh37_chr4:2948362-2949561 [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]
  • LOC116158484:CRISPRi-validated cis-regulatory element chr4.319 [Gene]
  • CTBP1-AS:CTBP1 antisense RNA [Gene - HGNC]
  • CTBP1-DT:CTBP1 divergent transcript [Gene - HGNC]
  • POLN:DNA polymerase nu [Gene - OMIM - HGNC]
  • HAUS3:HAUS augmin like complex subunit 3 [Gene - OMIM - HGNC]
  • MXD4:MAX dimerization protein 4 [Gene - OMIM - HGNC]
  • NAT8L:N-acetyltransferase 8 like [Gene - OMIM - HGNC]
  • NICOL1:NELL2 interacting cell ontogeny regulator 1 [Gene - OMIM - HGNC]
  • NKX1-1:NK1 homeobox 1 [Gene - OMIM - HGNC]
  • NOP14-AS1:NOP14 antisense RNA 1 [Gene - HGNC]
  • NOP14:NOP14 nucleolar protein [Gene - OMIM - HGNC]
  • LOC126806945:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:1388225-1389424 [Gene]
  • LOC126806947:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:2937390-2938589 [Gene]
  • PCGF3-AS1:PCGF3 antisense RNA 1 [Gene - HGNC]
  • PDE6B-AS1:PDE6B antisense RNA 1 [Gene - HGNC]
  • SH3BP2:SH3 domain binding protein 2 [Gene - OMIM - HGNC]
  • LOC123466218:Sharpr-MPRA regulatory region 1470 [Gene]
  • LOC114004383:Sharpr-MPRA regulatory region 3424 [Gene]
  • LOC123466219:Sharpr-MPRA regulatory region 6001 [Gene]
  • LOC114004382:Sharpr-MPRA regulatory region 8056 [Gene]
  • LOC123466217:Sharpr-MPRA regulatory region 8787 [Gene]
  • TNIP2:TNFAIP3 interacting protein 2 [Gene - OMIM - HGNC]
  • UVSSA:UV stimulated scaffold protein A [Gene - OMIM - HGNC]
  • LOC110120693:VISTA enhancer hs526 [Gene]
  • ADD1:adducin 1 [Gene - OMIM - HGNC]
  • IDUA:alpha-L-iduronidase [Gene - OMIM - HGNC]
  • CFAP99:cilia and flagella associated protein 99 [Gene - 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]
  • FAM193A:family with sequence similarity 193 member A [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]
  • MFSD10:major facilitator superfamily domain containing 10 [Gene - OMIM - HGNC]
  • MIR4800:microRNA 4800 [Gene - HGNC]
  • MIR943:microRNA 943 [Gene - HGNC]
  • MYL5:myosin light chain 5 [Gene - OMIM - HGNC]
  • NELFA:negative elongation factor complex member A [Gene - OMIM - HGNC]
  • LOC106804089:nonconserved acetylation island sequence 125 enhancer [Gene]
  • NSD2:nuclear receptor binding SET domain protein 2 [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]
  • RNF4:ring finger protein 4 [Gene - OMIM - HGNC]
  • SCARNA22:small Cajal body-specific RNA 22 [Gene - 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]
  • LOC100130872:uncharacterized LOC100130872 [Gene]
  • LOC105374344:uncharacterized LOC105374344 [Gene]
  • ZFYVE28:zinc finger FYVE-type containing 28 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
GRCh38/hg38 4p16.3(chr4:620566-2958209)x3
HGVS:
  • NC_000004.12:g.(?_620566)_(2958209_?)dup
  • NC_000004.10:g.(?_604355)_(2929734_?)dup
  • NC_000004.11:g.(?_614355)_(2959936_?)dup
Links:
dbVar: nssv578967; dbVar: nssv578968; dbVar: nsv529424
Observations:
2

Condition(s)

Name:
See cases [See the Variation display for details]
Identifiers:

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000078167ISCA site 4

See additional submitters

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes2not 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 ISCA site 4, SCV000078167.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
2not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedDiscovery1not providednot providednot provided
2unknownyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024