GRCh38/hg38 1q21.1-21.2(chr1:144572470-149076087)x1 AND See cases

Clinical significance:Likely pathogenic

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000141565.3

Allele description [Variation Report for GRCh38/hg38 1q21.1-21.2(chr1:144572470-149076087)x1]

GRCh38/hg38 1q21.1-21.2(chr1:144572470-149076087)x1

Genes:
  • BCL9:BCL9 transcription coactivator [Gene - OMIM - HGNC]
  • CD160:CD160 molecule [Gene - OMIM - HGNC]
  • GPR89A:G protein-coupled receptor 89A [Gene - OMIM - HGNC]
  • GPR89B:G protein-coupled receptor 89B [Gene - OMIM - HGNC]
  • LOC111556113:HNF4 motif-containing MPRA enhancer 9 [Gene]
  • LIX1L-AS1:LIX1L antisense RNA 1 [Gene - HGNC]
  • NBPF10:NBPF member 10 [Gene - OMIM - HGNC]
  • NBPF11:NBPF member 11 [Gene - OMIM - HGNC]
  • NBPF12:NBPF member 12 [Gene - OMIM - HGNC]
  • NBPF14:NBPF member 14 [Gene - OMIM - HGNC]
  • NBPF20:NBPF member 20 [Gene - OMIM - HGNC]
  • NBPF9:NBPF member 9 [Gene - OMIM - HGNC]
  • PDZK1:PDZ domain containing 1 [Gene - OMIM - HGNC]
  • LOC108254679:POLR3GL-TXNIP intergenic CAGE-defined low expression enhancer [Gene]
  • RBM8A:RNA binding motif protein 8A [Gene - OMIM - HGNC]
  • POLR3C:RNA polymerase III subunit C [Gene - OMIM - HGNC]
  • POLR3GL:RNA polymerase III subunit GL [Gene - OMIM - HGNC]
  • RNVU1-14:RNA, variant U1 small nuclear 14 [Gene - HGNC]
  • RNVU1-1:RNA, variant U1 small nuclear 1 [Gene - HGNC]
  • RNVU1-3:RNA, variant U1 small nuclear 3 [Gene - HGNC]
  • RNVU1-6:RNA, variant U1 small nuclear 6 [Gene - HGNC]
  • RNVU1-7:RNA, variant U1 small nuclear 7 [Gene - HGNC]
  • RNVU1-8:RNA, variant U1 small nuclear 8 [Gene - HGNC]
  • SRGAP2B:SLIT-ROBO Rho GTPase activating protein 2B [Gene - OMIM - HGNC]
  • LOC120893158:Sharpr-MPRA regulatory region 11936 [Gene]
  • LOC112577490:Sharpr-MPRA regulatory region 3868 [Gene]
  • LOC110121261:VISTA enhancer hs2126 [Gene]
  • ACP6:acid phosphatase 6, lysophosphatidic [Gene - OMIM - HGNC]
  • ANKRD34A:ankyrin repeat domain 34A [Gene - HGNC]
  • ANKRD35:ankyrin repeat domain 35 [Gene - HGNC]
  • CHD1L:chromodomain helicase DNA binding protein 1 like [Gene - OMIM - HGNC]
  • LOC106783502:conserved acetylation island sequence C12 enhancer [Gene]
  • FAM72D:family with sequence similarity 72 member D [Gene - OMIM - HGNC]
  • FMO5:flavin containing dimethylaniline monoxygenase 5 [Gene - OMIM - HGNC]
  • GJA5:gap junction protein alpha 5 [Gene - OMIM - HGNC]
  • GJA8:gap junction protein alpha 8 [Gene - OMIM - HGNC]
  • HJV:hemojuvelin BMP co-receptor [Gene - OMIM - HGNC]
  • ITGA10:integrin subunit alpha 10 [Gene - OMIM - HGNC]
  • LIX1L:limb and CNS expressed 1 like [Gene - HGNC]
  • LINC01138:long intergenic non-protein coding RNA 1138 [Gene - HGNC]
  • LINC01145:long intergenic non-protein coding RNA 1145 [Gene - HGNC]
  • LINC01719:long intergenic non-protein coding RNA 1719 [Gene - HGNC]
  • LINC01731:long intergenic non-protein coding RNA 1731 [Gene - HGNC]
  • LINC02804:long intergenic non-protein coding RNA 2804 [Gene - HGNC]
  • LINC02805:long intergenic non-protein coding RNA 2805 [Gene - HGNC]
  • LINC02806:long intergenic non-protein coding RNA 2806 [Gene - HGNC]
  • LINC00624:long intergenic non-protein coding RNA 624 [Gene - HGNC]
  • MIR5087:microRNA 5087 [Gene - HGNC]
  • MIR6077:microRNA 6077 [Gene - HGNC]
  • MIR6736:microRNA 6736 [Gene - HGNC]
  • NOTCH2NLA:notch 2 N-terminal like A [Gene - OMIM - HGNC]
  • NOTCH2NLB:notch 2 N-terminal like B [Gene - OMIM - HGNC]
  • NUDT17:nudix hydrolase 17 [Gene - HGNC]
  • NUDT4B:nudix hydrolase 4B [Gene - HGNC]
  • PPIAL4D:peptidylprolyl isomerase A like 4D [Gene - HGNC]
  • PPIAL4F:peptidylprolyl isomerase A like 4F [Gene - HGNC]
  • PPIAL4G:peptidylprolyl isomerase A like 4G [Gene - HGNC]
  • PPIAL4H:peptidylprolyl isomerase A like 4H [Gene - HGNC]
  • PEX11B:peroxisomal biogenesis factor 11 beta [Gene - OMIM - HGNC]
  • PDE4DIP:phosphodiesterase 4D interacting protein [Gene - OMIM - HGNC]
  • PIAS3:protein inhibitor of activated STAT 3 [Gene - OMIM - HGNC]
  • PRKAB2:protein kinase AMP-activated non-catalytic subunit beta 2 [Gene - OMIM - HGNC]
  • RNF115:ring finger protein 115 [Gene - HGNC]
  • TRN-GTT10-1:tRNA-Asn (anticodon GTT) 10-1 [Gene - HGNC]
  • TRN-GTT2-1:tRNA-Asn (anticodon GTT) 2-1 [Gene - HGNC]
  • TRN-GTT2-7:tRNA-Asn (anticodon GTT) 2-7 [Gene - OMIM - HGNC]
  • TRN-GTT24-1:tRNA-Asn (anticodon GTT) 24-1 [Gene - HGNC]
  • TRN-GTT9-1:tRNA-Asn (anticodon GTT) 9-1 [Gene - HGNC]
  • TRN-GTT9-2:tRNA-Asn (anticodon GTT) 9-2 [Gene - HGNC]
  • TRQ-CTG3-1:tRNA-Gln (anticodon CTG) 3-1 [Gene - HGNC]
  • TRQ-CTG3-2:tRNA-Gln (anticodon CTG) 3-2 [Gene - HGNC]
  • TRQ-CTG4-1:tRNA-Gln (anticodon CTG) 4-1 [Gene - HGNC]
  • TRQ-CTG7-1:tRNA-Gln (anticodon CTG) 7-1 [Gene - HGNC]
  • TRE-CTC1-1:tRNA-Glu (anticodon CTC) 1-1 [Gene - HGNC]
  • TRG-TCC2-1:tRNA-Gly (anticodon TCC) 2-1 [Gene - HGNC]
  • TRH-GTG1-1:tRNA-His (anticodon GTG) 1-1 [Gene - HGNC]
  • TRH-GTG1-2:tRNA-His (anticodon GTG) 1-2 [Gene - HGNC]
  • TRH-GTG1-3:tRNA-His (anticodon GTG) 1-3 [Gene - HGNC]
  • TRH-GTG1-4:tRNA-His (anticodon GTG) 1-4 [Gene - HGNC]
  • TRK-CTT2-1:tRNA-Lys (anticodon CTT) 2-1 [Gene - HGNC]
  • TXNIP:thioredoxin interacting protein [Gene - OMIM - HGNC]
  • LOC100996740:uncharacterized LOC100996740 [Gene]
  • LOC100996741:uncharacterized LOC100996741 [Gene]
  • LOC101927468:uncharacterized LOC101927468 [Gene]
  • CH17-408M7.1:uncharacterized LOC102724558 [Gene]
  • LOC105371215:uncharacterized LOC105371215 [Gene]
Variant type:
copy number loss
Cytogenetic location:
1q21.1-21.2
Genomic location:
Preferred name:
GRCh38/hg38 1q21.1-21.2(chr1:144572470-149076087)x1
HGVS:
  • NC_000001.11:g.(?_144572470)_(149076087_?)del
  • NC_000001.10:g.(?_146500972)_(148809863_?)del
  • NC_000001.9:g.(?_144967596)_(147076487_?)del
Links:
dbVar: nssv3395752; dbVar: nsv995065
Observations:
1

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000182482ISCA site 3

See additional submitters

no assertion criteria providedLikely pathogenicnot providedclinical testing

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

Description

Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter.

SCV000182482

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not 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 3, SCV000182482.3

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

Last Updated: May 19, 2021

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