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NC_000009.11:g.(?_138645763)_(140729425_?)del AND Kleefstra syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 10, 2019
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:
RCV001031921.9

Allele description [Variation Report for NC_000009.11:g.(?_138645763)_(140729425_?)del]

NC_000009.11:g.(?_138645763)_(140729425_?)del

Genes:
  • AGPAT2:1-acylglycerol-3-phosphate O-acyltransferase 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]
  • SEC16A:SEC16 homolog A, endoplasmic reticulum export factor [Gene - OMIM - HGNC]
  • SSNA1:SS nuclear autoantigen 1 [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]
  • 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]
  • 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]
  • 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]
  • 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]
  • FUT7:fucosyltransferase 7 [Gene - OMIM - HGNC]
  • GRIN1:glutamate ionotropic receptor NMDA type subunit 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]
  • LCN6:lipocalin 6 [Gene - OMIM - HGNC]
  • LCN8:lipocalin 8 [Gene - OMIM - HGNC]
  • LCNL1:lipocalin like 1 [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]
  • 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]
  • 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]
  • KCNT1:potassium sodium-activated channel subfamily T member 1 [Gene - OMIM - HGNC]
  • PTGDS:prostaglandin D2 synthase [Gene - OMIM - HGNC]
  • QSOX2:quiescin sulfhydryl oxidase 2 [Gene - OMIM - HGNC]
  • RNF208:ring finger protein 208 [Gene - OMIM - HGNC]
  • RNF224:ring finger protein 224 [Gene - HGNC]
  • SNAPC4:small nuclear RNA activating complex polypeptide 4 [Gene - OMIM - HGNC]
  • SNHG7:small nucleolar RNA host gene 7 [Gene - HGNC]
  • SLC34A3:solute carrier family 34 member 3 [Gene - OMIM - HGNC]
  • STPG3:sperm-tail PG-rich repeat containing 3 [Gene - HGNC]
  • SAPCD2:suppressor APC domain containing 2 [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]
  • ZMYND19:zinc finger MYND-type containing 19 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.3
Genomic location:
Chr9: 138645763 - 140729425 (on Assembly GRCh37)
Preferred name:
NC_000009.11:g.(?_138645763)_(140729425_?)del
HGVS:
NC_000009.11:g.(?_138645763)_(140729425_?)del

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
SCV001195228Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(May 10, 2019) 		germlineclinical testing

PubMed (3)
[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

Enrichment of small pathogenic deletions at chromosome 9p24.3 and 9q34.3 involving DOCK8, KANK1, EHMT1 genes identified by using high-resolution oligonucleotide-single nucleotide polymorphism array analysis.

Wang JC, Mahon LW, Ross LP, Anguiano A, Owen R, Boyar FZ.

Mol Cytogenet. 2016;9:82.

PubMed [citation]
PMID:
27891178
PMCID:
PMC5111223

Further clinical and molecular delineation of the 9q subtelomeric deletion syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype.

Kleefstra T, van Zelst-Stams WA, Nillesen WM, Cormier-Daire V, Houge G, Foulds N, van Dooren M, Willemsen MH, Pfundt R, Turner A, Wilson M, McGaughran J, Rauch A, Zenker M, Adam MP, Innes M, Davies C, López AG, Casalone R, Weber A, Brueton LA, Navarro AD, et al.

J Med Genet. 2009 Sep;46(9):598-606. doi: 10.1136/jmg.2008.062950. Epub 2009 Mar 4.

PubMed [citation]
PMID:
19264732
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001195228.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the EHMT1 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of EHMT1 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 19264732, 27891178). Loss-of-function variants in EHMT1 are known to be pathogenic (PMID: 16826528, 19264732). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 24, 2024