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GRCh38/hg38 9q34.3(chr9:136806104-138394717) AND Kleefstra syndrome 1

Germline classification:
Pathogenic (1 submission)
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:
RCV004720497.1

Allele description [Variation Report for GRCh38/hg38 9q34.3(chr9:136806104-138394717)]

GRCh38/hg38 9q34.3(chr9:136806104-138394717)

Genes:
  • LOC108254695:9q34.3 CACNA1B recombination region [Gene]
  • LOC108281115:9q34.3 EHMT1 distal recombination region [Gene]
  • LOC108281113:9q34.3 PNPLA7 recombination region [Gene]
  • LOC108281114:9q34.3 TOR4A distal recombination region [Gene]
  • ARRDC1-AS1:ARRDC1 antisense RNA 1 [Gene - HGNC]
  • LOC130003047:ATAC-STARR-seq lymphoblastoid active region 29329 [Gene]
  • LOC130003052:ATAC-STARR-seq lymphoblastoid active region 29330 [Gene]
  • LOC130003053:ATAC-STARR-seq lymphoblastoid active region 29331 [Gene]
  • LOC130003054:ATAC-STARR-seq lymphoblastoid active region 29332 [Gene]
  • LOC130003055:ATAC-STARR-seq lymphoblastoid active region 29333 [Gene]
  • LOC130003056:ATAC-STARR-seq lymphoblastoid active region 29334 [Gene]
  • LOC130003058:ATAC-STARR-seq lymphoblastoid active region 29335 [Gene]
  • LOC130003059:ATAC-STARR-seq lymphoblastoid active region 29336 [Gene]
  • LOC130003065:ATAC-STARR-seq lymphoblastoid active region 29337 [Gene]
  • LOC130003066:ATAC-STARR-seq lymphoblastoid active region 29338 [Gene]
  • LOC130003078:ATAC-STARR-seq lymphoblastoid active region 29343 [Gene]
  • LOC130003080:ATAC-STARR-seq lymphoblastoid active region 29344 [Gene]
  • LOC130003083:ATAC-STARR-seq lymphoblastoid active region 29345 [Gene]
  • LOC130003086:ATAC-STARR-seq lymphoblastoid active region 29346 [Gene]
  • LOC130003090:ATAC-STARR-seq lymphoblastoid active region 29347 [Gene]
  • LOC130003102:ATAC-STARR-seq lymphoblastoid active region 29349 [Gene]
  • LOC130003107:ATAC-STARR-seq lymphoblastoid active region 29350 [Gene]
  • LOC130003124:ATAC-STARR-seq lymphoblastoid active region 29352 [Gene]
  • LOC130003127:ATAC-STARR-seq lymphoblastoid active region 29354 [Gene]
  • LOC130003134:ATAC-STARR-seq lymphoblastoid active region 29355 [Gene]
  • LOC130003136:ATAC-STARR-seq lymphoblastoid active region 29356 [Gene]
  • LOC130003137:ATAC-STARR-seq lymphoblastoid active region 29357 [Gene]
  • LOC130003138:ATAC-STARR-seq lymphoblastoid active region 29358 [Gene]
  • LOC130003139:ATAC-STARR-seq lymphoblastoid active region 29359 [Gene]
  • LOC130003141:ATAC-STARR-seq lymphoblastoid active region 29361 [Gene]
  • LOC130003142:ATAC-STARR-seq lymphoblastoid active region 29362 [Gene]
  • LOC130003143:ATAC-STARR-seq lymphoblastoid active region 29363 [Gene]
  • LOC130003144:ATAC-STARR-seq lymphoblastoid active region 29364 [Gene]
  • LOC130003145:ATAC-STARR-seq lymphoblastoid active region 29366 [Gene]
  • LOC130003146:ATAC-STARR-seq lymphoblastoid active region 29367 [Gene]
  • LOC130003147:ATAC-STARR-seq lymphoblastoid active region 29368 [Gene]
  • LOC130003148:ATAC-STARR-seq lymphoblastoid active region 29369 [Gene]
  • LOC130003149:ATAC-STARR-seq lymphoblastoid active region 29370 [Gene]
  • LOC130003150:ATAC-STARR-seq lymphoblastoid active region 29371 [Gene]
  • LOC130003040:ATAC-STARR-seq lymphoblastoid silent region 20546 [Gene]
  • LOC130003041:ATAC-STARR-seq lymphoblastoid silent region 20547 [Gene]
  • LOC130003042:ATAC-STARR-seq lymphoblastoid silent region 20549 [Gene]
  • LOC130003043:ATAC-STARR-seq lymphoblastoid silent region 20550 [Gene]
  • LOC130003044:ATAC-STARR-seq lymphoblastoid silent region 20551 [Gene]
  • LOC130003045:ATAC-STARR-seq lymphoblastoid silent region 20552 [Gene]
  • LOC130003046:ATAC-STARR-seq lymphoblastoid silent region 20553 [Gene]
  • LOC130003048:ATAC-STARR-seq lymphoblastoid silent region 20554 [Gene]
  • LOC130003049:ATAC-STARR-seq lymphoblastoid silent region 20555 [Gene]
  • LOC130003050:ATAC-STARR-seq lymphoblastoid silent region 20556 [Gene]
  • LOC130003051:ATAC-STARR-seq lymphoblastoid silent region 20557 [Gene]
  • LOC130003057:ATAC-STARR-seq lymphoblastoid silent region 20558 [Gene]
  • LOC130003060:ATAC-STARR-seq lymphoblastoid silent region 20561 [Gene]
  • LOC130003061:ATAC-STARR-seq lymphoblastoid silent region 20562 [Gene]
  • LOC130003062:ATAC-STARR-seq lymphoblastoid silent region 20563 [Gene]
  • LOC130003063:ATAC-STARR-seq lymphoblastoid silent region 20564 [Gene]
  • LOC130003064:ATAC-STARR-seq lymphoblastoid silent region 20565 [Gene]
  • LOC130003067:ATAC-STARR-seq lymphoblastoid silent region 20567 [Gene]
  • LOC130003068:ATAC-STARR-seq lymphoblastoid silent region 20568 [Gene]
  • LOC130003069:ATAC-STARR-seq lymphoblastoid silent region 20569 [Gene]
  • LOC130003070:ATAC-STARR-seq lymphoblastoid silent region 20571 [Gene]
  • LOC130003071:ATAC-STARR-seq lymphoblastoid silent region 20572 [Gene]
  • LOC130003072:ATAC-STARR-seq lymphoblastoid silent region 20573 [Gene]
  • LOC130003073:ATAC-STARR-seq lymphoblastoid silent region 20574 [Gene]
  • LOC130003074:ATAC-STARR-seq lymphoblastoid silent region 20575 [Gene]
  • LOC130003075:ATAC-STARR-seq lymphoblastoid silent region 20576 [Gene]
  • LOC130003076:ATAC-STARR-seq lymphoblastoid silent region 20577 [Gene]
  • LOC130003077:ATAC-STARR-seq lymphoblastoid silent region 20578 [Gene]
  • LOC130003079:ATAC-STARR-seq lymphoblastoid silent region 20579 [Gene]
  • LOC130003081:ATAC-STARR-seq lymphoblastoid silent region 20580 [Gene]
  • LOC130003082:ATAC-STARR-seq lymphoblastoid silent region 20581 [Gene]
  • LOC130003084:ATAC-STARR-seq lymphoblastoid silent region 20582 [Gene]
  • LOC130003085:ATAC-STARR-seq lymphoblastoid silent region 20583 [Gene]
  • LOC130003087:ATAC-STARR-seq lymphoblastoid silent region 20585 [Gene]
  • LOC130003088:ATAC-STARR-seq lymphoblastoid silent region 20586 [Gene]
  • LOC130003089:ATAC-STARR-seq lymphoblastoid silent region 20587 [Gene]
  • LOC130003091:ATAC-STARR-seq lymphoblastoid silent region 20588 [Gene]
  • LOC130003092:ATAC-STARR-seq lymphoblastoid silent region 20589 [Gene]
  • LOC130003093:ATAC-STARR-seq lymphoblastoid silent region 20590 [Gene]
  • LOC130003094:ATAC-STARR-seq lymphoblastoid silent region 20591 [Gene]
  • LOC130003095:ATAC-STARR-seq lymphoblastoid silent region 20592 [Gene]
  • LOC130003096:ATAC-STARR-seq lymphoblastoid silent region 20593 [Gene]
  • LOC130003097:ATAC-STARR-seq lymphoblastoid silent region 20594 [Gene]
  • LOC130003098:ATAC-STARR-seq lymphoblastoid silent region 20596 [Gene]
  • LOC130003099:ATAC-STARR-seq lymphoblastoid silent region 20597 [Gene]
  • LOC130003100:ATAC-STARR-seq lymphoblastoid silent region 20598 [Gene]
  • LOC130003101:ATAC-STARR-seq lymphoblastoid silent region 20599 [Gene]
  • LOC130003103:ATAC-STARR-seq lymphoblastoid silent region 20604 [Gene]
  • LOC130003104:ATAC-STARR-seq lymphoblastoid silent region 20605 [Gene]
  • LOC130003105:ATAC-STARR-seq lymphoblastoid silent region 20606 [Gene]
  • LOC130003106:ATAC-STARR-seq lymphoblastoid silent region 20607 [Gene]
  • LOC130003108:ATAC-STARR-seq lymphoblastoid silent region 20608 [Gene]
  • LOC130003109:ATAC-STARR-seq lymphoblastoid silent region 20609 [Gene]
  • LOC130003110:ATAC-STARR-seq lymphoblastoid silent region 20610 [Gene]
  • LOC130003111:ATAC-STARR-seq lymphoblastoid silent region 20611 [Gene]
  • LOC130003112:ATAC-STARR-seq lymphoblastoid silent region 20613 [Gene]
  • LOC130003113:ATAC-STARR-seq lymphoblastoid silent region 20614 [Gene]
  • LOC130003114:ATAC-STARR-seq lymphoblastoid silent region 20615 [Gene]
  • LOC130003115:ATAC-STARR-seq lymphoblastoid silent region 20616 [Gene]
  • LOC130003116:ATAC-STARR-seq lymphoblastoid silent region 20619 [Gene]
  • LOC130003117:ATAC-STARR-seq lymphoblastoid silent region 20620 [Gene]
  • LOC130003118:ATAC-STARR-seq lymphoblastoid silent region 20621 [Gene]
  • LOC130003119:ATAC-STARR-seq lymphoblastoid silent region 20623 [Gene]
  • LOC130003120:ATAC-STARR-seq lymphoblastoid silent region 20624 [Gene]
  • LOC130003121:ATAC-STARR-seq lymphoblastoid silent region 20625 [Gene]
  • LOC130003122:ATAC-STARR-seq lymphoblastoid silent region 20626 [Gene]
  • LOC130003123:ATAC-STARR-seq lymphoblastoid silent region 20627 [Gene]
  • LOC130003125:ATAC-STARR-seq lymphoblastoid silent region 20628 [Gene]
  • LOC130003126:ATAC-STARR-seq lymphoblastoid silent region 20629 [Gene]
  • LOC130003128:ATAC-STARR-seq lymphoblastoid silent region 20630 [Gene]
  • LOC130003129:ATAC-STARR-seq lymphoblastoid silent region 20631 [Gene]
  • LOC130003130:ATAC-STARR-seq lymphoblastoid silent region 20632 [Gene]
  • LOC130003131:ATAC-STARR-seq lymphoblastoid silent region 20633 [Gene]
  • LOC130003132:ATAC-STARR-seq lymphoblastoid silent region 20634 [Gene]
  • LOC130003133:ATAC-STARR-seq lymphoblastoid silent region 20635 [Gene]
  • LOC130003135:ATAC-STARR-seq lymphoblastoid silent region 20636 [Gene]
  • LOC130003140:ATAC-STARR-seq lymphoblastoid silent region 20637 [Gene]
  • ABCA2:ATP binding cassette subfamily A member 2 [Gene - OMIM - HGNC]
  • CACNA1B-AS1:CACNA1B antisense RNA 1 [Gene - HGNC]
  • CCDC183-AS1:CCDC183 antisense RNA 1 [Gene - HGNC]
  • LOC126860796:CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139904888-139906087 [Gene]
  • LOC126860799:CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:140657628-140658827 [Gene]
  • LOC126860801:CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:140884423-140885622 [Gene]
  • FBXW5:F-box and WD repeat domain containing 5 [Gene - OMIM - HGNC]
  • MAMDC4:MAM domain containing 4 [Gene - OMIM - HGNC]
  • MAN1B1-DT:MAN1B1 divergent transcript [Gene - HGNC]
  • LOC126860797:MED14-independent group 3 enhancer GRCh37_chr9:140343721-140344920 [Gene]
  • LOC126860798:MED14-independent group 3 enhancer GRCh37_chr9:140377541-140378740 [Gene]
  • LOC126860800:MED14-independent group 3 enhancer GRCh37_chr9:140767993-140769192 [Gene]
  • LOC129390118:MPRA-validated peak7347 silencer [Gene]
  • 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]
  • SSNA1:SS nuclear autoantigen 1 [Gene - OMIM - HGNC]
  • STPG3-AS1:STPG3 antisense RNA 1 [Gene - HGNC]
  • LOC124375253:Sharpr-MPRA regulatory region 12030 [Gene]
  • LOC121366035:Sharpr-MPRA regulatory region 13741 [Gene]
  • LOC124375249:Sharpr-MPRA regulatory region 3127 [Gene]
  • LOC113839542:Sharpr-MPRA regulatory region 4489 [Gene]
  • LOC124375252:Sharpr-MPRA regulatory region 4638 [Gene]
  • LOC124375251:Sharpr-MPRA regulatory region 5016 [Gene]
  • LOC124375248:Sharpr-MPRA regulatory region 5679 [Gene]
  • LOC121366036:Sharpr-MPRA regulatory region 6441 [Gene]
  • LOC124375250:Sharpr-MPRA regulatory region 8071 [Gene]
  • LOC124375254:Sharpr-MPRA regulatory region 8502 [Gene]
  • TRAF2:TNF receptor associated factor 2 [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]
  • CACNA1B:calcium voltage-gated channel subunit alpha1 B [Gene - OMIM - HGNC]
  • CLIC3:chloride intracellular channel 3 [Gene - OMIM - 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]
  • ENTPD2:ectonucleoside triphosphate diphosphohydrolase 2 [Gene - OMIM - HGNC]
  • ENTPD8:ectonucleoside triphosphate diphosphohydrolase 8 [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]
  • FAM157B:family with sequence similarity 157 member B [Gene - HGNC]
  • FUT7:fucosyltransferase 7 [Gene - OMIM - HGNC]
  • GRIN1:glutamate ionotropic receptor NMDA type subunit 1 [Gene - OMIM - HGNC]
  • LRRC26:leucine rich repeat containing 26 [Gene - OMIM - HGNC]
  • LCN12:lipocalin 12 [Gene - OMIM - HGNC]
  • LCNL1:lipocalin like 1 [Gene - HGNC]
  • LINC02692:long intergenic non-protein coding RNA 2692 [Gene - HGNC]
  • LINC02908:long intergenic non-protein coding RNA 2908 [Gene - HGNC]
  • MAN1B1:mannosidase alpha class 1B member 1 [Gene - OMIM - HGNC]
  • MIR3621:microRNA 3621 [Gene - HGNC]
  • MIR4292:microRNA 4292 [Gene - HGNC]
  • MIR4479:microRNA 4479 [Gene - HGNC]
  • MIR602:microRNA 602 [Gene - HGNC]
  • MIR7114:microRNA 7114 [Gene - 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]
  • PNPLA7:patatin like phospholipase domain containing 7 [Gene - OMIM - HGNC]
  • PHPT1:phosphohistidine phosphatase 1 [Gene - OMIM - HGNC]
  • PTGDS:prostaglandin D2 synthase [Gene - OMIM - HGNC]
  • RNF208:ring finger protein 208 [Gene - OMIM - HGNC]
  • RNF224:ring finger protein 224 [Gene - HGNC]
  • LOC122513141:ring finger protein-like [Gene]
  • 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]
  • TMEM203:transmembrane protein 203 [Gene - OMIM - HGNC]
  • TMEM210:transmembrane protein 210 [Gene - HGNC]
  • TUBB4B:tubulin beta 4B class IVb [Gene - OMIM - HGNC]
  • LOC100133077:uncharacterized LOC100133077 [Gene]
  • LOC101928786:uncharacterized LOC101928786 [Gene]
  • LOC101928932:uncharacterized LOC101928932 [Gene]
  • LOC651337:uncharacterized LOC651337 [Gene]
  • ZMYND19:zinc finger MYND-type containing 19 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
9q34.3
Genomic location:
Chr9: 136805464 - 138394717 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 9q34.3(chr9:136806104-138394717)

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
SCV005049597Laboratory of Genetics, Children's Clinical University Hospital Latvia
criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)		Pathogenicgermlinecuration

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedcuration

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

Comprehensive EHMT1 variants analysis broadens genotype-phenotype associations and molecular mechanisms in Kleefstra syndrome.

Rots D, Bouman A, Yamada A, Levy M, Dingemans AJM, de Vries BBA, Ruiterkamp-Versteeg M, de Leeuw N, Ockeloen CW, Pfundt R, de Boer E, Kummeling J, van Bon B, van Bokhoven H, Kasri NN, Venselaar H, Alders M, Kerkhof J, McConkey H, Kuechler A, Elffers B, van Beeck Calkoen R, et al.

Am J Hum Genet. 2024 Aug 8;111(8):1605-1625. doi: 10.1016/j.ajhg.2024.06.008. Epub 2024 Jul 15.

PubMed [citation]
PMID:
39013458
PMCID:
PMC11339614

Details of each submission

From Laboratory of Genetics, Children's Clinical University Hospital Latvia, SCV005049597.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024