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NC_000009.11:g.(?_136218768)_(141016451_?)dup AND Kleefstra syndrome 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 8, 2022
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:
RCV003122719.4

Allele description [Variation Report for NC_000009.11:g.(?_136218768)_(141016451_?)dup]

NC_000009.11:g.(?_136218768)_(141016451_?)dup

Genes:
  • AGPAT2:1-acylglycerol-3-phosphate O-acyltransferase 2 [Gene - OMIM - HGNC]
  • ADAMTS13:ADAM metallopeptidase with thrombospondin type 1 motif 13 [Gene - OMIM - HGNC]
  • ADAMTSL2:ADAMTS like 2 [Gene - OMIM - HGNC]
  • ABCA2:ATP binding cassette subfamily A member 2 [Gene - OMIM - HGNC]
  • DNLZ:DNL-type zinc finger [Gene - OMIM - HGNC]
  • EGFL7:EGF like domain multiple 7 [Gene - OMIM - HGNC]
  • FBXW5:F-box and WD repeat domain containing 5 [Gene - OMIM - HGNC]
  • GPSM1:G protein signaling modulator 1 [Gene - OMIM - HGNC]
  • LHX3:LIM homeobox 3 [Gene - OMIM - HGNC]
  • MAMDC4:MAM domain containing 4 [Gene - OMIM - HGNC]
  • NACC2:NACC family member 2 [Gene - OMIM - HGNC]
  • NDOR1:NADPH dependent diflavin oxidoreductase 1 [Gene - OMIM - HGNC]
  • NOXA1:NADPH oxidase activator 1 [Gene - OMIM - HGNC]
  • NSMF:NMDA receptor synaptonuclear signaling and neuronal migration factor [Gene - OMIM - HGNC]
  • NRARP:NOTCH regulated ankyrin repeat protein [Gene - OMIM - HGNC]
  • PAXX:PAXX non-homologous end joining factor [Gene - OMIM - HGNC]
  • RABL6:RAB, member RAS oncogene family like 6 [Gene - OMIM - HGNC]
  • REXO4:REX4 homolog, 3'-5' exonuclease [Gene - OMIM - HGNC]
  • RNU6ATAC:RNA, U6atac small nuclear [Gene - OMIM - HGNC]
  • SEC16A:SEC16 homolog A, endoplasmic reticulum export factor [Gene - OMIM - HGNC]
  • SSNA1:SS nuclear autoantigen 1 [Gene - OMIM - HGNC]
  • SURF1:SURF1 cytochrome c oxidase assembly factor [Gene - OMIM - HGNC]
  • TRAF2:TNF receptor associated factor 2 [Gene - OMIM - HGNC]
  • UBAC1:UBA domain containing 1 [Gene - OMIM - HGNC]
  • UAP1L1:UDP-N-acetylglucosamine pyrophosphorylase 1 like 1 [Gene - HGNC]
  • WDR5:WD repeat domain 5 [Gene - OMIM - HGNC]
  • ANAPC2:anaphase promoting complex subunit 2 [Gene - OMIM - HGNC]
  • AJM1:apical junction component 1 homolog [Gene - HGNC]
  • ARRDC1:arrestin domain containing 1 [Gene - OMIM - HGNC]
  • BRD3:bromodomain containing 3 [Gene - OMIM - HGNC]
  • CACFD1:calcium channel flower domain containing 1 [Gene - OMIM - HGNC]
  • CACNA1B:calcium voltage-gated channel subunit alpha1 B [Gene - OMIM - HGNC]
  • CAMSAP1:calmodulin regulated spectrin associated protein 1 [Gene - OMIM - HGNC]
  • CARD9:caspase recruitment domain family member 9 [Gene - OMIM - HGNC]
  • CLIC3:chloride intracellular channel 3 [Gene - OMIM - HGNC]
  • C9orf163:chromosome 9 putative open reading frame 163 [Gene - HGNC]
  • CIMIP2A:ciliary microtubule inner protein 2A [Gene - HGNC]
  • CCDC183:coiled-coil domain containing 183 [Gene - OMIM - HGNC]
  • COL5A1:collagen type V alpha 1 chain [Gene - OMIM - HGNC]
  • C8G:complement C8 gamma chain [Gene - OMIM - HGNC]
  • CYSRT1:cysteine rich tail 1 [Gene - HGNC]
  • DPP7:dipeptidyl peptidase 7 [Gene - OMIM - HGNC]
  • DPH7:diphthamide biosynthesis 7 [Gene - OMIM - HGNC]
  • DIPK1B:divergent protein kinase domain 1B [Gene - OMIM - HGNC]
  • DBH:dopamine beta-hydroxylase [Gene - OMIM - HGNC]
  • ENTPD2:ectonucleoside triphosphate diphosphohydrolase 2 [Gene - OMIM - HGNC]
  • ENTPD8:ectonucleoside triphosphate diphosphohydrolase 8 [Gene - OMIM - HGNC]
  • ENTR1:endosome associated trafficking regulator 1 [Gene - OMIM - HGNC]
  • EDF1:endothelial differentiation related factor 1 [Gene - OMIM - HGNC]
  • EHMT1:euchromatic histone lysine methyltransferase 1 [Gene - OMIM - HGNC]
  • EXD3:exonuclease 3'-5' domain containing 3 [Gene - OMIM - HGNC]
  • FAM163B:family with sequence similarity 163 member B [Gene - HGNC]
  • FCN1:ficolin 1 [Gene - OMIM - HGNC]
  • FCN2:ficolin 2 [Gene - OMIM - HGNC]
  • FUT7:fucosyltransferase 7 [Gene - OMIM - HGNC]
  • GRIN1:glutamate ionotropic receptor NMDA type subunit 1 [Gene - OMIM - HGNC]
  • GLT6D1:glycosyltransferase 6 domain containing 1 [Gene - OMIM - HGNC]
  • INPP5E:inositol polyphosphate-5-phosphatase E [Gene - OMIM - HGNC]
  • LRRC26:leucine rich repeat containing 26 [Gene - OMIM - HGNC]
  • LCN10:lipocalin 10 [Gene - OMIM - HGNC]
  • LCN12:lipocalin 12 [Gene - OMIM - HGNC]
  • LCN15:lipocalin 15 [Gene - HGNC]
  • LCN1:lipocalin 1 [Gene - OMIM - HGNC]
  • LCN6:lipocalin 6 [Gene - OMIM - HGNC]
  • LCN8:lipocalin 8 [Gene - OMIM - HGNC]
  • LCN9:lipocalin 9 [Gene - OMIM - HGNC]
  • LCNL1:lipocalin like 1 [Gene - HGNC]
  • LINC02907:long intergenic non-protein coding RNA 2907 [Gene - HGNC]
  • LINC02908:long intergenic non-protein coding RNA 2908 [Gene - HGNC]
  • MAN1B1:mannosidase alpha class 1B member 1 [Gene - OMIM - HGNC]
  • MIR126:microRNA 126 [Gene - OMIM - HGNC]
  • MRPL41:mitochondrial ribosomal protein L41 [Gene - OMIM - HGNC]
  • MRPS2:mitochondrial ribosomal protein S2 [Gene - OMIM - HGNC]
  • MYMK:myomaker, myoblast fusion factor [Gene - OMIM - HGNC]
  • NELFB:negative elongation factor complex member B [Gene - OMIM - HGNC]
  • NPDC1:neural proliferation, differentiation and control 1 [Gene - OMIM - HGNC]
  • NOTCH1:notch receptor 1 [Gene - OMIM - HGNC]
  • OBP2A:odorant binding protein 2A [Gene - OMIM - HGNC]
  • OLFM1:olfactomedin 1 [Gene - OMIM - HGNC]
  • PNPLA7:patatin like phospholipase domain containing 7 [Gene - OMIM - HGNC]
  • PMPCA:peptidase, mitochondrial processing subunit alpha [Gene - OMIM - HGNC]
  • PHPT1:phosphohistidine phosphatase 1 [Gene - OMIM - HGNC]
  • PIERCE1:piercer of microtubule wall 1 [Gene - OMIM - HGNC]
  • KCNT1:potassium sodium-activated channel subfamily T member 1 [Gene - OMIM - HGNC]
  • PAEP:progestagen associated endometrial protein [Gene - OMIM - HGNC]
  • PTGDS:prostaglandin D2 synthase [Gene - OMIM - HGNC]
  • PPP1R26:protein phosphatase 1 regulatory subunit 26 [Gene - OMIM - HGNC]
  • QSOX2:quiescin sulfhydryl oxidase 2 [Gene - OMIM - HGNC]
  • RXRA:retinoid X receptor alpha [Gene - OMIM - HGNC]
  • RNF208:ring finger protein 208 [Gene - OMIM - HGNC]
  • RNF224:ring finger protein 224 [Gene - HGNC]
  • SARDH:sarcosine dehydrogenase [Gene - OMIM - HGNC]
  • STKLD1:serine/threonine kinase like domain containing 1 [Gene - OMIM - HGNC]
  • SNAPC4:small nuclear RNA activating complex polypeptide 4 [Gene - OMIM - HGNC]
  • SNHG7:small nucleolar RNA host gene 7 [Gene - HGNC]
  • SLC2A6:solute carrier family 2 member 6 [Gene - OMIM - HGNC]
  • SLC34A3:solute carrier family 34 member 3 [Gene - OMIM - HGNC]
  • STPG3:sperm-tail PG-rich repeat containing 3 [Gene - HGNC]
  • SOHLH1:spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Gene - OMIM - HGNC]
  • SAPCD2:suppressor APC domain containing 2 [Gene - OMIM - HGNC]
  • SURF2:surfeit 2 [Gene - OMIM - HGNC]
  • SURF4:surfeit 4 [Gene - OMIM - HGNC]
  • TPRN:taperin [Gene - OMIM - HGNC]
  • TOR4A:torsin family 4 member A [Gene - HGNC]
  • TMEM141:transmembrane protein 141 [Gene - HGNC]
  • TMEM203:transmembrane protein 203 [Gene - OMIM - HGNC]
  • TMEM210:transmembrane protein 210 [Gene - HGNC]
  • TMEM250:transmembrane protein 250 [Gene - HGNC]
  • TUBB4B:tubulin beta 4B class IVb [Gene - OMIM - HGNC]
  • LOC651337:uncharacterized LOC651337 [Gene]
  • VAV2:vav guanine nucleotide exchange factor 2 [Gene - OMIM - HGNC]
  • ZMYND19:zinc finger MYND-type containing 19 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
9q34.2-34.3
Genomic location:
Chr9: 136218768 - 141016451 (on Assembly GRCh37)
Preferred name:
NC_000009.11:g.(?_136218768)_(141016451_?)dup
HGVS:
NC_000009.11:g.(?_136218768)_(141016451_?)dup

Condition(s)

Name:
Kleefstra syndrome 1
Identifiers:
MONDO: MONDO:0027407; MedGen: C0795833; Orphanet: 261494; OMIM: 610253

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003795566Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 8, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Human gene copy number spectra analysis in congenital heart malformations.

Tomita-Mitchell A, Mahnke DK, Struble CA, Tuffnell ME, Stamm KD, Hidestrand M, Harris SE, Goetsch MA, Simpson PM, Bick DP, Broeckel U, Pelech AN, Tweddell JS, Mitchell ME.

Physiol Genomics. 2012 May 1;44(9):518-41. doi: 10.1152/physiolgenomics.00013.2012. Epub 2012 Feb 7.

PubMed [citation]
PMID:
22318994
PMCID:
PMC3426426

Human subtelomeric copy number gains suggest a DNA replication mechanism for formation: beyond breakage-fusion-bridge for telomere stabilization.

Yatsenko SA, Hixson P, Roney EK, Scott DA, Schaaf CP, Ng YT, Palmer R, Fisher RB, Patel A, Cheung SW, Lupski JR.

Hum Genet. 2012 Dec;131(12):1895-910. doi: 10.1007/s00439-012-1216-9. Epub 2012 Aug 14.

PubMed [citation]
PMID:
22890305
PMCID:
PMC3493700
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003795566.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

A copy number gain of the genomic region encompassing the full coding sequence of the EHMT1 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. Isolated whole-gene copy number gains of EHMT1 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 22318994, 22890305, 31209758). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024