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GRCh38/hg38 12q14.2-15(chr12:63871239-67314524) AND Silver-Russell syndrome 5

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 1, 2024
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:
RCV004547403.1

Allele description [Variation Report for GRCh38/hg38 12q14.2-15(chr12:63871239-67314524)]

GRCh38/hg38 12q14.2-15(chr12:63871239-67314524)

Genes:
  • LOC130008196:ATAC-STARR-seq lymphoblastoid active region 6586 [Gene]
  • LOC130008197:ATAC-STARR-seq lymphoblastoid active region 6587 [Gene]
  • LOC130008198:ATAC-STARR-seq lymphoblastoid active region 6588 [Gene]
  • LOC130008199:ATAC-STARR-seq lymphoblastoid active region 6591 [Gene]
  • LOC130008200:ATAC-STARR-seq lymphoblastoid active region 6592 [Gene]
  • LOC130008204:ATAC-STARR-seq lymphoblastoid active region 6593 [Gene]
  • LOC130008205:ATAC-STARR-seq lymphoblastoid active region 6594 [Gene]
  • LOC130008206:ATAC-STARR-seq lymphoblastoid active region 6595 [Gene]
  • LOC130008207:ATAC-STARR-seq lymphoblastoid active region 6596 [Gene]
  • LOC130008211:ATAC-STARR-seq lymphoblastoid active region 6597 [Gene]
  • LOC130008212:ATAC-STARR-seq lymphoblastoid active region 6599 [Gene]
  • LOC130008213:ATAC-STARR-seq lymphoblastoid active region 6600 [Gene]
  • LOC130008217:ATAC-STARR-seq lymphoblastoid active region 6601 [Gene]
  • LOC130008218:ATAC-STARR-seq lymphoblastoid active region 6602 [Gene]
  • LOC130008219:ATAC-STARR-seq lymphoblastoid active region 6603 [Gene]
  • LOC130008220:ATAC-STARR-seq lymphoblastoid active region 6604 [Gene]
  • LOC130008222:ATAC-STARR-seq lymphoblastoid active region 6605 [Gene]
  • LOC130008223:ATAC-STARR-seq lymphoblastoid active region 6606 [Gene]
  • LOC130008225:ATAC-STARR-seq lymphoblastoid active region 6608 [Gene]
  • LOC130008229:ATAC-STARR-seq lymphoblastoid active region 6609 [Gene]
  • LOC130008230:ATAC-STARR-seq lymphoblastoid active region 6610 [Gene]
  • LOC130008231:ATAC-STARR-seq lymphoblastoid active region 6611 [Gene]
  • LOC130008232:ATAC-STARR-seq lymphoblastoid active region 6612 [Gene]
  • LOC130008233:ATAC-STARR-seq lymphoblastoid active region 6613 [Gene]
  • LOC130008236:ATAC-STARR-seq lymphoblastoid active region 6615 [Gene]
  • LOC130008238:ATAC-STARR-seq lymphoblastoid active region 6616 [Gene]
  • LOC130008239:ATAC-STARR-seq lymphoblastoid active region 6617 [Gene]
  • LOC130008240:ATAC-STARR-seq lymphoblastoid active region 6618 [Gene]
  • LOC130008241:ATAC-STARR-seq lymphoblastoid active region 6619 [Gene]
  • LOC130008242:ATAC-STARR-seq lymphoblastoid active region 6620 [Gene]
  • LOC130008243:ATAC-STARR-seq lymphoblastoid active region 6621 [Gene]
  • LOC130008245:ATAC-STARR-seq lymphoblastoid active region 6622 [Gene]
  • LOC130008247:ATAC-STARR-seq lymphoblastoid active region 6623 [Gene]
  • LOC130008248:ATAC-STARR-seq lymphoblastoid active region 6624 [Gene]
  • LOC130008201:ATAC-STARR-seq lymphoblastoid silent region 4619 [Gene]
  • LOC130008202:ATAC-STARR-seq lymphoblastoid silent region 4620 [Gene]
  • LOC130008203:ATAC-STARR-seq lymphoblastoid silent region 4621 [Gene]
  • LOC130008208:ATAC-STARR-seq lymphoblastoid silent region 4622 [Gene]
  • LOC130008209:ATAC-STARR-seq lymphoblastoid silent region 4623 [Gene]
  • LOC130008210:ATAC-STARR-seq lymphoblastoid silent region 4624 [Gene]
  • LOC130008214:ATAC-STARR-seq lymphoblastoid silent region 4626 [Gene]
  • LOC130008215:ATAC-STARR-seq lymphoblastoid silent region 4627 [Gene]
  • LOC130008216:ATAC-STARR-seq lymphoblastoid silent region 4628 [Gene]
  • LOC130008221:ATAC-STARR-seq lymphoblastoid silent region 4629 [Gene]
  • LOC130008224:ATAC-STARR-seq lymphoblastoid silent region 4630 [Gene]
  • LOC130008226:ATAC-STARR-seq lymphoblastoid silent region 4631 [Gene]
  • LOC130008227:ATAC-STARR-seq lymphoblastoid silent region 4632 [Gene]
  • LOC130008228:ATAC-STARR-seq lymphoblastoid silent region 4633 [Gene]
  • LOC130008234:ATAC-STARR-seq lymphoblastoid silent region 4635 [Gene]
  • LOC130008235:ATAC-STARR-seq lymphoblastoid silent region 4636 [Gene]
  • LOC130008237:ATAC-STARR-seq lymphoblastoid silent region 4637 [Gene]
  • LOC130008244:ATAC-STARR-seq lymphoblastoid silent region 4638 [Gene]
  • LOC130008246:ATAC-STARR-seq lymphoblastoid silent region 4639 [Gene]
  • LOC126861558:BRD4-independent group 4 enhancer GRCh37_chr12:65950046-65951245 [Gene]
  • HELB:DNA helicase B [Gene - OMIM - HGNC]
  • HMGA2-AS1:HMGA2 antisense RNA 1 [Gene - HGNC]
  • LOC111365214:HNF4 motif-containing MPRA enhancer 102 [Gene]
  • KICS2:KICSTOR subunit 2 [Gene - OMIM - HGNC]
  • LEMD3:LEM domain containing 3 [Gene - OMIM - HGNC]
  • LLPH:LLP homolog, long-term synaptic facilitation factor [Gene - OMIM - HGNC]
  • LLPH-DT:LLPH divergent transcript [Gene - HGNC]
  • LOC129390470:MPRA-validated peak1758 silencer [Gene]
  • LOC129390471:MPRA-validated peak1761 silencer [Gene]
  • LOC129390472:MPRA-validated peak1765 silencer [Gene]
  • LOC129390473:MPRA-validated peak1767 silencer [Gene]
  • LOC129390474:MPRA-validated peak1768 silencer [Gene]
  • LOC129390475:MPRA-validated peak1769 silencer [Gene]
  • LOC129390476:MPRA-validated peak1770 silencer [Gene]
  • LOC129390477:MPRA-validated peak1773 silencer [Gene]
  • MSRB3-AS1:MSRB3 antisense RNA 1 [Gene - HGNC]
  • LOC126861555:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:64574933-64576132 [Gene]
  • LOC126861556:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:65824313-65825512 [Gene]
  • LOC126861557:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:65930061-65931260 [Gene]
  • LOC126861559:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:66050206-66051405 [Gene]
  • RASSF3-DT:RASSF3 divergent transcript [Gene - HGNC]
  • RASSF3:Ras association domain family member 3 [Gene - OMIM - HGNC]
  • SRGAP1:SLIT-ROBO Rho GTPase activating protein 1 [Gene - OMIM - HGNC]
  • LOC121832841:Sharpr-MPRA regulatory region 11590 [Gene]
  • LOC124629392:Sharpr-MPRA regulatory region 14888 [Gene]
  • LOC124629394:Sharpr-MPRA regulatory region 15140 [Gene]
  • LOC121832840:Sharpr-MPRA regulatory region 2861 [Gene]
  • LOC124629391:Sharpr-MPRA regulatory region 4654 [Gene]
  • LOC124629399:Sharpr-MPRA regulatory region 5579 [Gene]
  • LOC124629395:Sharpr-MPRA regulatory region 869 [Gene]
  • LOC124629393:Sharpr-MPRA regulatory region 9176 [Gene]
  • TBK1:TANK binding kinase 1 [Gene - OMIM - HGNC]
  • TBC1D30:TBC1 domain family member 30 [Gene - OMIM - HGNC]
  • LOC110121381:VISTA enhancer hs1498 [Gene]
  • WIF1:WNT inhibitory factor 1 [Gene - OMIM - HGNC]
  • C12orf56:chromosome 12 open reading frame 56 [Gene - HGNC]
  • CAND1:cullin associated and neddylation dissociated 1 [Gene - OMIM - HGNC]
  • XPOT:exportin for tRNA [Gene - OMIM - HGNC]
  • GNS:glucosamine (N-acetyl)-6-sulfatase [Gene - OMIM - HGNC]
  • GRIP1:glutamate receptor interacting protein 1 [Gene - OMIM - HGNC]
  • HMGA2:high mobility group AT-hook 2 [Gene - OMIM - HGNC]
  • IRAK3:interleukin 1 receptor associated kinase 3 [Gene - OMIM - HGNC]
  • LINC02231:long intergenic non-protein coding RNA 2231 [Gene - HGNC]
  • LINC02389:long intergenic non-protein coding RNA 2389 [Gene - HGNC]
  • LINC02425:long intergenic non-protein coding RNA 2425 [Gene - HGNC]
  • LINC02454:long intergenic non-protein coding RNA 2454 [Gene - HGNC]
  • MSRB3:methionine sulfoxide reductase B3 [Gene - OMIM - HGNC]
  • MIR548C:microRNA 548c [Gene - HGNC]
  • MIR548Z:microRNA 548z [Gene - HGNC]
  • MIR6074:microRNA 6074 [Gene - HGNC]
  • MIR6502:microRNA 6502 [Gene - HGNC]
  • LOC120766155:negCOR silencer S1 [Gene]
  • TMBIM4:transmembrane BAX inhibitor motif containing 4 [Gene - OMIM - HGNC]
  • LOC102724421:uncharacterized LOC102724421 [Gene]
  • LOC105369187:uncharacterized LOC105369187 [Gene]
  • LOC105369803:uncharacterized LOC105369803 [Gene]
Variant type:
copy number loss
Cytogenetic location:
12q14.2-15
Genomic location:
Chr12: 63871180 - 67314583 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 12q14.2-15(chr12:63871239-67314524)
Observations:
1

Condition(s)

Name:
Silver-Russell syndrome 5 (SRS5)
Identifiers:
MONDO: MONDO:0020795; MedGen: C5394456; OMIM: 618908

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005039004Department Of Biochemistry, Hamamatsu University School Of Medicine
criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)		Uncertain significance
(May 1, 2024) 		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

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]
PMID:
31690835
PMCID:
PMC7313390

Details of each submission

From Department Of Biochemistry, Hamamatsu University School Of Medicine, SCV005039004.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

Last Updated: May 19, 2024