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GRCh38/hg38 3p26.3-26.1(chr3:52266-4827490)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 16, 2011
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:
RCV000142736.5

Allele description [Variation Report for GRCh38/hg38 3p26.3-26.1(chr3:52266-4827490)x1]

GRCh38/hg38 3p26.3-26.1(chr3:52266-4827490)x1

Genes:
  • LOC129936036:ATAC-STARR-seq lymphoblastoid active region 19334 [Gene]
  • LOC129936037:ATAC-STARR-seq lymphoblastoid active region 19335 [Gene]
  • LOC129936038:ATAC-STARR-seq lymphoblastoid active region 19336 [Gene]
  • LOC129936039:ATAC-STARR-seq lymphoblastoid active region 19337 [Gene]
  • LOC129936040:ATAC-STARR-seq lymphoblastoid active region 19338 [Gene]
  • LOC129936041:ATAC-STARR-seq lymphoblastoid active region 19339 [Gene]
  • LOC129936042:ATAC-STARR-seq lymphoblastoid active region 19340 [Gene]
  • LOC129936043:ATAC-STARR-seq lymphoblastoid active region 19342 [Gene]
  • LOC129936046:ATAC-STARR-seq lymphoblastoid active region 19343 [Gene]
  • LOC129936049:ATAC-STARR-seq lymphoblastoid active region 19345 [Gene]
  • LOC129936053:ATAC-STARR-seq lymphoblastoid active region 19346 [Gene]
  • LOC129936055:ATAC-STARR-seq lymphoblastoid active region 19347 [Gene]
  • LOC129936057:ATAC-STARR-seq lymphoblastoid active region 19348 [Gene]
  • LOC129936060:ATAC-STARR-seq lymphoblastoid active region 19349 [Gene]
  • LOC129936061:ATAC-STARR-seq lymphoblastoid active region 19350 [Gene]
  • LOC129936062:ATAC-STARR-seq lymphoblastoid active region 19351 [Gene]
  • LOC129936063:ATAC-STARR-seq lymphoblastoid active region 19352 [Gene]
  • LOC129936064:ATAC-STARR-seq lymphoblastoid active region 19353 [Gene]
  • LOC129936065:ATAC-STARR-seq lymphoblastoid active region 19354 [Gene]
  • LOC129936066:ATAC-STARR-seq lymphoblastoid active region 19355 [Gene]
  • LOC129936035:ATAC-STARR-seq lymphoblastoid silent region 14006 [Gene]
  • LOC129936044:ATAC-STARR-seq lymphoblastoid silent region 14007 [Gene]
  • LOC129936045:ATAC-STARR-seq lymphoblastoid silent region 14008 [Gene]
  • LOC129936047:ATAC-STARR-seq lymphoblastoid silent region 14009 [Gene]
  • LOC129936048:ATAC-STARR-seq lymphoblastoid silent region 14010 [Gene]
  • LOC129936050:ATAC-STARR-seq lymphoblastoid silent region 14011 [Gene]
  • LOC129936051:ATAC-STARR-seq lymphoblastoid silent region 14012 [Gene]
  • LOC129936052:ATAC-STARR-seq lymphoblastoid silent region 14013 [Gene]
  • LOC129936054:ATAC-STARR-seq lymphoblastoid silent region 14015 [Gene]
  • LOC129936056:ATAC-STARR-seq lymphoblastoid silent region 14016 [Gene]
  • LOC129936058:ATAC-STARR-seq lymphoblastoid silent region 14017 [Gene]
  • LOC129936059:ATAC-STARR-seq lymphoblastoid silent region 14018 [Gene]
  • LOC126806587:BRD4-independent group 4 enhancer GRCh37_chr3:1277185-1278384 [Gene]
  • LOC126806588:BRD4-independent group 4 enhancer GRCh37_chr3:3079797-3080996 [Gene]
  • LOC126806585:CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:118683-119882 [Gene]
  • CHL1-AS1:CHL1 antisense RNA 1 [Gene - HGNC]
  • CHL1-AS2:CHL1 antisense RNA 2 [Gene - HGNC]
  • CNTN4-AS1:CNTN4 antisense RNA 1 [Gene - HGNC]
  • CNTN4-AS2:CNTN4 antisense RNA 2 [Gene - HGNC]
  • LOC111429626:FOXA motif-containing MPRA enhancer 226 [Gene]
  • ITPR1-DT:ITPR1 divergent transcript [Gene - HGNC]
  • LOC126806586:MED14-independent group 3 enhancer GRCh37_chr3:152955-154154 [Gene]
  • LOC126806589:MED14-independent group 3 enhancer GRCh37_chr3:3600748-3601947 [Gene]
  • LOC126806590:MED14-independent group 3 enhancer GRCh37_chr3:4855759-4856958 [Gene]
  • LOC129389017:MPRA-validated peak4526 silencer [Gene]
  • LOC132088944:Neanderthal introgressed variant-containing enhancer experimental_68491 [Gene]
  • LOC132088949:Neanderthal introgressed variant-containing enhancer experimental_68954 [Gene]
  • LOC132088954:Neanderthal introgressed variant-containing enhancer experimental_69430 [Gene]
  • LOC132088963:Neanderthal introgressed variant-containing enhancer experimental_69928 [Gene]
  • LOC132088964:Neanderthal introgressed variant-containing enhancer experimental_69934 [Gene]
  • LOC132088965:Neanderthal introgressed variant-containing enhancer experimental_69968 [Gene]
  • SETMAR:SET domain and mariner transposase fusion gene [Gene - OMIM - HGNC]
  • LOC122889018:Sharpr-MPRA regulatory region 107 [Gene]
  • LOC122889020:Sharpr-MPRA regulatory region 12228 [Gene]
  • LOC122889019:Sharpr-MPRA regulatory region 14120 [Gene]
  • LOC112935932:Sharpr-MPRA regulatory region 14798 [Gene]
  • LOC112935931:Sharpr-MPRA regulatory region 4455 [Gene]
  • LOC121725127:Sharpr-MPRA regulatory region 6601 [Gene]
  • LOC122889021:Sharpr-MPRA regulatory region 7157 [Gene]
  • LOC122889017:Sharpr-MPRA regulatory region 9777 [Gene]
  • CHL1:cell adhesion molecule L1 like [Gene - OMIM - HGNC]
  • CRBN:cereblon [Gene - OMIM - HGNC]
  • CNTN4:contactin 4 [Gene - OMIM - HGNC]
  • CNTN6:contactin 6 [Gene - OMIM - HGNC]
  • EGOT:eosinophil granule ontogeny transcript [Gene - OMIM - HGNC]
  • ITPR1:inositol 1,4,5-trisphosphate receptor type 1 [Gene - OMIM - HGNC]
  • IL5RA:interleukin 5 receptor subunit alpha [Gene - OMIM - HGNC]
  • LRRN1:leucine rich repeat neuronal 1 [Gene - OMIM - HGNC]
  • LINC01266:long intergenic non-protein coding RNA 1266 [Gene - HGNC]
  • LOC107522035:meiotic recombination hotspot S [Gene]
  • LOC107522028:meiotic recombination hotspot T [Gene]
  • SUMF1:sulfatase modifying factor 1 [Gene - OMIM - HGNC]
  • TRNT1:tRNA nucleotidyl transferase 1 [Gene - OMIM - HGNC]
  • LOC100130207:uncharacterized LOC100130207 [Gene]
Variant type:
copy number loss
Cytogenetic location:
3p26.3-26.1
Genomic location:
Preferred name:
GRCh38/hg38 3p26.3-26.1(chr3:52266-4827490)x1
HGVS:
  • NC_000003.12:g.(?_52266)_(4827490_?)del
  • NC_000003.10:g.(?_68949)_(4844174_?)del
  • NC_000003.11:g.(?_93949)_(4869174_?)del
Links:
dbVar: nssv582361; dbVar: nsv534353
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
SCV000177129ISCA site 2

See additional submitters

no assertion criteria provided
Pathogenic
(Sep 16, 2011) 		de novoclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]
PMID:
20466091
PMCID:
PMC2869000

Details of each submission

From ISCA site 2, SCV000177129.3

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

Last Updated: May 7, 2024