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GRCh38/hg38 4q31.21-31.3(chr4:140876253-152186578)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:
RCV000051787.5

Allele description [Variation Report for GRCh38/hg38 4q31.21-31.3(chr4:140876253-152186578)x3]

GRCh38/hg38 4q31.21-31.3(chr4:140876253-152186578)x3

Genes:
  • LOC129993131:ATAC-STARR-seq lymphoblastoid active region 21938 [Gene]
  • LOC129993132:ATAC-STARR-seq lymphoblastoid active region 21939 [Gene]
  • LOC129993133:ATAC-STARR-seq lymphoblastoid active region 21940 [Gene]
  • LOC129993134:ATAC-STARR-seq lymphoblastoid active region 21941 [Gene]
  • LOC129993137:ATAC-STARR-seq lymphoblastoid active region 21942 [Gene]
  • LOC129993138:ATAC-STARR-seq lymphoblastoid active region 21943 [Gene]
  • LOC129993139:ATAC-STARR-seq lymphoblastoid active region 21944 [Gene]
  • LOC129993140:ATAC-STARR-seq lymphoblastoid active region 21945 [Gene]
  • LOC129993141:ATAC-STARR-seq lymphoblastoid active region 21946 [Gene]
  • LOC129993142:ATAC-STARR-seq lymphoblastoid active region 21947 [Gene]
  • LOC129993143:ATAC-STARR-seq lymphoblastoid active region 21948 [Gene]
  • LOC129993144:ATAC-STARR-seq lymphoblastoid active region 21949 [Gene]
  • LOC129993145:ATAC-STARR-seq lymphoblastoid active region 21950 [Gene]
  • LOC129993146:ATAC-STARR-seq lymphoblastoid active region 21951 [Gene]
  • LOC129993147:ATAC-STARR-seq lymphoblastoid active region 21952 [Gene]
  • LOC129993148:ATAC-STARR-seq lymphoblastoid active region 21953 [Gene]
  • LOC129993149:ATAC-STARR-seq lymphoblastoid active region 21954 [Gene]
  • LOC129993150:ATAC-STARR-seq lymphoblastoid active region 21955 [Gene]
  • LOC129993151:ATAC-STARR-seq lymphoblastoid active region 21956 [Gene]
  • LOC129993152:ATAC-STARR-seq lymphoblastoid active region 21957 [Gene]
  • LOC129993153:ATAC-STARR-seq lymphoblastoid active region 21958 [Gene]
  • LOC129993155:ATAC-STARR-seq lymphoblastoid active region 21962 [Gene]
  • LOC129993156:ATAC-STARR-seq lymphoblastoid active region 21963 [Gene]
  • LOC129993157:ATAC-STARR-seq lymphoblastoid active region 21964 [Gene]
  • LOC129993165:ATAC-STARR-seq lymphoblastoid active region 21965 [Gene]
  • LOC129993166:ATAC-STARR-seq lymphoblastoid active region 21966 [Gene]
  • LOC129993168:ATAC-STARR-seq lymphoblastoid active region 21967 [Gene]
  • LOC129993169:ATAC-STARR-seq lymphoblastoid active region 21969 [Gene]
  • LOC129993170:ATAC-STARR-seq lymphoblastoid active region 21970 [Gene]
  • LOC129993172:ATAC-STARR-seq lymphoblastoid active region 21971 [Gene]
  • LOC129993176:ATAC-STARR-seq lymphoblastoid active region 21972 [Gene]
  • LOC129993178:ATAC-STARR-seq lymphoblastoid active region 21973 [Gene]
  • LOC129993179:ATAC-STARR-seq lymphoblastoid active region 21974 [Gene]
  • LOC129993180:ATAC-STARR-seq lymphoblastoid active region 21976 [Gene]
  • LOC129993181:ATAC-STARR-seq lymphoblastoid active region 21977 [Gene]
  • LOC129993182:ATAC-STARR-seq lymphoblastoid active region 21978 [Gene]
  • LOC129993183:ATAC-STARR-seq lymphoblastoid active region 21979 [Gene]
  • LOC129993184:ATAC-STARR-seq lymphoblastoid active region 21980 [Gene]
  • LOC129993186:ATAC-STARR-seq lymphoblastoid active region 21981 [Gene]
  • LOC129993187:ATAC-STARR-seq lymphoblastoid active region 21982 [Gene]
  • LOC129993188:ATAC-STARR-seq lymphoblastoid active region 21983 [Gene]
  • LOC129993189:ATAC-STARR-seq lymphoblastoid active region 21984 [Gene]
  • LOC129993190:ATAC-STARR-seq lymphoblastoid active region 21985 [Gene]
  • LOC129993191:ATAC-STARR-seq lymphoblastoid active region 21986 [Gene]
  • LOC129993192:ATAC-STARR-seq lymphoblastoid active region 21987 [Gene]
  • LOC129993193:ATAC-STARR-seq lymphoblastoid active region 21988 [Gene]
  • LOC129993194:ATAC-STARR-seq lymphoblastoid active region 21992 [Gene]
  • LOC129993195:ATAC-STARR-seq lymphoblastoid active region 21993 [Gene]
  • LOC129993196:ATAC-STARR-seq lymphoblastoid active region 21994 [Gene]
  • LOC129993197:ATAC-STARR-seq lymphoblastoid active region 21995 [Gene]
  • LOC129993198:ATAC-STARR-seq lymphoblastoid active region 21996 [Gene]
  • LOC129993199:ATAC-STARR-seq lymphoblastoid active region 21997 [Gene]
  • LOC129993201:ATAC-STARR-seq lymphoblastoid active region 21998 [Gene]
  • LOC129993202:ATAC-STARR-seq lymphoblastoid active region 21999 [Gene]
  • LOC129993203:ATAC-STARR-seq lymphoblastoid active region 22000 [Gene]
  • LOC129993204:ATAC-STARR-seq lymphoblastoid active region 22001 [Gene]
  • LOC129993205:ATAC-STARR-seq lymphoblastoid active region 22002 [Gene]
  • LOC129993206:ATAC-STARR-seq lymphoblastoid active region 22003 [Gene]
  • LOC129993207:ATAC-STARR-seq lymphoblastoid active region 22005 [Gene]
  • LOC129993208:ATAC-STARR-seq lymphoblastoid active region 22006 [Gene]
  • LOC129993209:ATAC-STARR-seq lymphoblastoid active region 22007 [Gene]
  • LOC129993210:ATAC-STARR-seq lymphoblastoid active region 22008 [Gene]
  • LOC129993211:ATAC-STARR-seq lymphoblastoid active region 22009 [Gene]
  • LOC129993212:ATAC-STARR-seq lymphoblastoid active region 22010 [Gene]
  • LOC129993213:ATAC-STARR-seq lymphoblastoid active region 22011 [Gene]
  • LOC129993214:ATAC-STARR-seq lymphoblastoid active region 22012 [Gene]
  • LOC129993216:ATAC-STARR-seq lymphoblastoid active region 22013 [Gene]
  • LOC129993219:ATAC-STARR-seq lymphoblastoid active region 22014 [Gene]
  • LOC129993220:ATAC-STARR-seq lymphoblastoid active region 22015 [Gene]
  • LOC129993221:ATAC-STARR-seq lymphoblastoid active region 22016 [Gene]
  • LOC129993222:ATAC-STARR-seq lymphoblastoid active region 22017 [Gene]
  • LOC129993223:ATAC-STARR-seq lymphoblastoid active region 22018 [Gene]
  • LOC129993224:ATAC-STARR-seq lymphoblastoid active region 22019 [Gene]
  • LOC129993225:ATAC-STARR-seq lymphoblastoid active region 22022 [Gene]
  • LOC129993226:ATAC-STARR-seq lymphoblastoid active region 22023 [Gene]
  • LOC129993227:ATAC-STARR-seq lymphoblastoid active region 22024 [Gene]
  • LOC129993228:ATAC-STARR-seq lymphoblastoid active region 22025 [Gene]
  • LOC129993230:ATAC-STARR-seq lymphoblastoid active region 22026 [Gene]
  • LOC129993231:ATAC-STARR-seq lymphoblastoid active region 22027 [Gene]
  • LOC129993232:ATAC-STARR-seq lymphoblastoid active region 22028 [Gene]
  • LOC129993130:ATAC-STARR-seq lymphoblastoid silent region 15715 [Gene]
  • LOC129993135:ATAC-STARR-seq lymphoblastoid silent region 15719 [Gene]
  • LOC129993136:ATAC-STARR-seq lymphoblastoid silent region 15720 [Gene]
  • LOC129993154:ATAC-STARR-seq lymphoblastoid silent region 15722 [Gene]
  • LOC129993158:ATAC-STARR-seq lymphoblastoid silent region 15726 [Gene]
  • LOC129993159:ATAC-STARR-seq lymphoblastoid silent region 15727 [Gene]
  • LOC129993160:ATAC-STARR-seq lymphoblastoid silent region 15728 [Gene]
  • LOC129993161:ATAC-STARR-seq lymphoblastoid silent region 15729 [Gene]
  • LOC129993162:ATAC-STARR-seq lymphoblastoid silent region 15730 [Gene]
  • LOC129993163:ATAC-STARR-seq lymphoblastoid silent region 15731 [Gene]
  • LOC129993164:ATAC-STARR-seq lymphoblastoid silent region 15732 [Gene]
  • LOC129993167:ATAC-STARR-seq lymphoblastoid silent region 15733 [Gene]
  • LOC129993171:ATAC-STARR-seq lymphoblastoid silent region 15734 [Gene]
  • LOC129993173:ATAC-STARR-seq lymphoblastoid silent region 15735 [Gene]
  • LOC129993174:ATAC-STARR-seq lymphoblastoid silent region 15736 [Gene]
  • LOC129993175:ATAC-STARR-seq lymphoblastoid silent region 15737 [Gene]
  • LOC129993177:ATAC-STARR-seq lymphoblastoid silent region 15738 [Gene]
  • LOC129993185:ATAC-STARR-seq lymphoblastoid silent region 15739 [Gene]
  • LOC129993200:ATAC-STARR-seq lymphoblastoid silent region 15740 [Gene]
  • LOC129993215:ATAC-STARR-seq lymphoblastoid silent region 15744 [Gene]
  • LOC129993217:ATAC-STARR-seq lymphoblastoid silent region 15745 [Gene]
  • LOC129993218:ATAC-STARR-seq lymphoblastoid silent region 15746 [Gene]
  • LOC129993229:ATAC-STARR-seq lymphoblastoid silent region 15749 [Gene]
  • LOC129993233:ATAC-STARR-seq lymphoblastoid silent region 15750 [Gene]
  • ABCE1:ATP binding cassette subfamily E member 1 [Gene - OMIM - HGNC]
  • LOC126807170:BRD4-independent group 4 enhancer GRCh37_chr4:142252666-142253865 [Gene]
  • LOC126807180:BRD4-independent group 4 enhancer GRCh37_chr4:147878312-147879511 [Gene]
  • LOC126807181:BRD4-independent group 4 enhancer GRCh37_chr4:147880304-147881503 [Gene]
  • LOC126807187:BRD4-independent group 4 enhancer GRCh37_chr4:150015556-150016755 [Gene]
  • LOC126807188:BRD4-independent group 4 enhancer GRCh37_chr4:150262096-150263295 [Gene]
  • LOC126807171:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:142501441-142502640 [Gene]
  • LOC126807174:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:146220501-146221700 [Gene]
  • LOC126807184:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:148752558-148753757 [Gene]
  • LOC126807189:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:150329764-150330963 [Gene]
  • LOC126807191:CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:152236121-152237320 [Gene]
  • FHIP1A:FHF complex subunit HOOK interacting protein 1A [Gene - HGNC]
  • FHIP1A-DT:FHIP1A divergent transcript [Gene - HGNC]
  • FREM3:FRAS1 related extracellular matrix 3 [Gene - OMIM - HGNC]
  • GAB1:GRB2 associated binding protein 1 [Gene - OMIM - HGNC]
  • HHIP-AS1:HHIP antisense RNA 1 [Gene - HGNC]
  • IQCM:IQ motif containing M [Gene - HGNC]
  • LOC127898557:LOC105377488-LOC127898556 [Gene]
  • LRBA:LPS responsive beige-like anchor protein [Gene - OMIM - HGNC]
  • LOC108281188:LRBA intron ENCODE-defined enhancer [Gene]
  • LSM6:LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated [Gene - OMIM - HGNC]
  • LOC126807172:MED14-independent group 3 enhancer GRCh37_chr4:144358834-144360033 [Gene]
  • LOC126807173:MED14-independent group 3 enhancer GRCh37_chr4:146018722-146019921 [Gene]
  • LOC126807178:MED14-independent group 3 enhancer GRCh37_chr4:147143236-147144435 [Gene]
  • LOC126807179:MED14-independent group 3 enhancer GRCh37_chr4:147250043-147251242 [Gene]
  • LOC126807182:MED14-independent group 3 enhancer GRCh37_chr4:148213466-148214665 [Gene]
  • LOC126807183:MED14-independent group 3 enhancer GRCh37_chr4:148381637-148382836 [Gene]
  • LOC126807185:MED14-independent group 3 enhancer GRCh37_chr4:149113429-149114628 [Gene]
  • LOC126807186:MED14-independent group 3 enhancer GRCh37_chr4:149836481-149837680 [Gene]
  • LOC126807190:MED14-independent group 3 enhancer GRCh37_chr4:152020037-152021236 [Gene]
  • LOC129389239:MPRA-validated peak5125 silencer [Gene]
  • LOC129389240:MPRA-validated peak5130 silencer [Gene]
  • LOC129389241:MPRA-validated peak5131 silencer [Gene]
  • LOC129389242:MPRA-validated peak5133 silencer [Gene]
  • OTUD4:OTU deubiquitinase 4 [Gene - OMIM - HGNC]
  • LOC126807175:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:146729136-146730335 [Gene]
  • LOC126807176:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:146875811-146877010 [Gene]
  • LOC126807177:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:146975373-146976572 [Gene]
  • LOC126807192:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:153022858-153024057 [Gene]
  • LOC126807193:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:153027165-153028364 [Gene]
  • POU4F2:POU class 4 homeobox 2 [Gene - OMIM - HGNC]
  • ARHGAP10:Rho GTPase activating protein 10 [Gene - OMIM - HGNC]
  • SH3D19:SH3 domain containing 19 [Gene - OMIM - HGNC]
  • SMAD1:SMAD family member 1 [Gene - OMIM - HGNC]
  • SMAD1-AS1:SMAD1 antisense RNA 1 [Gene - HGNC]
  • SMAD1-AS2:SMAD1 antisense RNA 2 [Gene - HGNC]
  • SMARCA5-AS1:SMARCA5 antisense RNA 1 [Gene - HGNC]
  • SMARCA5:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 [Gene - OMIM - HGNC]
  • LOC123480944:Sharpr-MPRA regulatory region 13307 [Gene]
  • LOC123493216:Sharpr-MPRA regulatory region 13510 [Gene]
  • LOC123480945:Sharpr-MPRA regulatory region 14262 [Gene]
  • LOC112939919:Sharpr-MPRA regulatory region 2118 [Gene]
  • LOC123493219:Sharpr-MPRA regulatory region 2958 [Gene]
  • LOC121056744:Sharpr-MPRA regulatory region 3738 [Gene]
  • LOC123493217:Sharpr-MPRA regulatory region 5429 [Gene]
  • LOC112939920:Sharpr-MPRA regulatory region 7108 [Gene]
  • LOC123480943:Sharpr-MPRA regulatory region 7410 [Gene]
  • LOC123493218:Sharpr-MPRA regulatory region 7547 [Gene]
  • TMEM184C-DT:TMEM184C divergent transcript [Gene - HGNC]
  • USP38-DT:USP38 divergent transcript [Gene - HGNC]
  • LOC110121159:VISTA enhancer hs1614 [Gene]
  • LOC110121259:VISTA enhancer hs2100 [Gene]
  • LOC110120799:VISTA enhancer hs906 [Gene]
  • ANAPC10:anaphase promoting complex subunit 10 [Gene - OMIM - HGNC]
  • C4orf51:chromosome 4 open reading frame 51 [Gene - HGNC]
  • DCLK2:doublecortin like kinase 2 [Gene - OMIM - HGNC]
  • EDNRA:endothelin receptor type A [Gene - OMIM - HGNC]
  • GATB:glutamyl-tRNA amidotransferase subunit B [Gene - OMIM - HGNC]
  • GYPA:glycophorin A (MNS blood group) [Gene - OMIM - HGNC]
  • GYPB:glycophorin B (MNS blood group) [Gene - OMIM - HGNC]
  • GYPE:glycophorin E (MNS blood group) [Gene - OMIM - HGNC]
  • HHIP:hedgehog interacting protein [Gene - OMIM - HGNC]
  • INPP4B:inositol polyphosphate-4-phosphatase type II B [Gene - OMIM - HGNC]
  • IL15:interleukin 15 [Gene - OMIM - HGNC]
  • LINC01095:long intergenic non-protein coding RNA 1095 [Gene - HGNC]
  • LINC02266:long intergenic non-protein coding RNA 2266 [Gene - HGNC]
  • LINC02273:long intergenic non-protein coding RNA 2273 [Gene - HGNC]
  • LINC02276:long intergenic non-protein coding RNA 2276 [Gene - HGNC]
  • LINC02355:long intergenic non-protein coding RNA 2355 [Gene - HGNC]
  • LINC02432:long intergenic non-protein coding RNA 2432 [Gene - HGNC]
  • LINC02491:long intergenic non-protein coding RNA 2491 [Gene - HGNC]
  • LINC02507:long intergenic non-protein coding RNA 2507 [Gene - HGNC]
  • LINC03074:long intergenic non-protein coding RNA 3074 [Gene - HGNC]
  • MAB21L2:mab-21 like 2 [Gene - OMIM - HGNC]
  • MMAA:metabolism of cobalamin associated A [Gene - OMIM - HGNC]
  • MIR3139:microRNA 3139 [Gene - HGNC]
  • MIR4799:microRNA 4799 [Gene - HGNC]
  • MIR548G:microRNA 548g [Gene - HGNC]
  • MIR7849:microRNA 7849 [Gene - HGNC]
  • NR3C2:nuclear receptor subfamily 3 group C member 2 [Gene - OMIM - HGNC]
  • PRMT9:protein arginine methyltransferase 9 [Gene - OMIM - HGNC]
  • REELD1:reeler domain containing 1 [Gene - HGNC]
  • RPS3A:ribosomal protein S3A [Gene - OMIM - HGNC]
  • RNF150:ring finger protein 150 [Gene - HGNC]
  • PRSS48:serine protease 48 [Gene - HGNC]
  • SNORD73A:small nucleolar RNA, C/D box 73A [Gene - OMIM - HGNC]
  • SNORD73B:small nucleolar RNA, C/D box U73B [Gene - HGNC]
  • SLC10A7:solute carrier family 10 member 7 [Gene - OMIM - HGNC]
  • TTC29:tetratricopeptide repeat domain 29 [Gene - OMIM - HGNC]
  • TMEM184C:transmembrane protein 184C [Gene - OMIM - HGNC]
  • USP38:ubiquitin specific peptidase 38 [Gene - OMIM - HGNC]
  • LOC101927636:uncharacterized LOC101927636 [Gene]
  • LOC102724700:uncharacterized LOC102724700 [Gene]
  • LOC105377458:uncharacterized LOC105377458 [Gene]
  • LOC105377468:uncharacterized LOC105377468 [Gene]
  • LOC105377473:uncharacterized LOC105377473 [Gene]
  • LOC105377480:uncharacterized LOC105377480 [Gene]
  • LOC105377488:uncharacterized LOC105377488 [Gene]
  • LOC127898556:uncharacterized LOC127898556 [Gene]
  • LOC729558:uncharacterized LOC729558 [Gene]
  • ZNF330:zinc finger protein 330 [Gene - OMIM - HGNC]
  • ZNF827:zinc finger protein 827 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
4q31.21-31.3
Genomic location:
Preferred name:
GRCh38/hg38 4q31.21-31.3(chr4:140876253-152186578)x3
HGVS:
  • NC_000004.12:g.(?_140876253)_(152186578_?)dup
  • NC_000004.10:g.(?_142016857)_(153327180_?)dup
  • NC_000004.11:g.(?_141797407)_(153107730_?)dup
Links:
dbVar: nssv578985; dbVar: nsv530308
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
SCV000079135GeneDx
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, SCV000079135.5

#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