NC_000019.9:g.(?_10828919)_(13482613_?)dup AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 6, 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:: RCV003109234.2

Allele description

NC_000019.9:g.(?_10828919)_(13482613_?)dup

Genes:

DAND5:DAN domain BMP antagonist family member 5 [Gene - OMIM - HGNC]
ECSIT:ECSIT signaling integrator [Gene - OMIM - HGNC]
ELAVL3:ELAV like RNA binding protein 3 [Gene - OMIM - HGNC]
FBXW9:F-box and WD repeat domain containing 9 [Gene - OMIM - HGNC]
GADD45GIP1:GADD45G interacting protein 1 [Gene - OMIM - HGNC]
JUNB:JunB proto-oncogene, AP-1 transcription factor subunit [Gene - OMIM - HGNC]
KLF1:KLF transcription factor 1 [Gene - OMIM - HGNC]
KANK2:KN motif and ankyrin repeat domains 2 [Gene - OMIM - HGNC]
LYL1:LYL1 basic helix-loop-helix family member [Gene - OMIM - HGNC]
RAB3D:RAB3D, member RAS oncogene family [Gene - OMIM - HGNC]
RAD23A:RAD23 homolog A, nucleotide excision repair protein [Gene - OMIM - HGNC]
SPC24:SPC24 component of NDC80 kinetochore complex [Gene - OMIM - HGNC]
SMARCA4:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 [Gene - OMIM - HGNC]
SWSAP1:SWIM-type zinc finger 7 associated protein 1 [Gene - OMIM - HGNC]
WDR83OS:WD repeat domain 83 opposite strand [Gene - OMIM - HGNC]
WDR83:WD repeat domain 83 [Gene - OMIM - HGNC]
YIPF2:Yip1 domain family member 2 [Gene - OMIM - HGNC]
ACP5:acid phosphatase 5, tartrate resistant [Gene - OMIM - HGNC]
ANGPTL8:angiopoietin like 8 [Gene - OMIM - HGNC]
BEST2:bestrophin 2 [Gene - OMIM - HGNC]
CACNA1A:calcium voltage-gated channel subunit alpha1 A [Gene - OMIM - HGNC]
CNN1:calponin 1 [Gene - OMIM - HGNC]
CALR:calreticulin [Gene - OMIM - HGNC]
C19orf38:chromosome 19 open reading frame 38 [Gene - HGNC]
CARM1:coactivator associated arginine methyltransferase 1 [Gene - OMIM - HGNC]
CCDC159:coiled-coil domain containing 159 [Gene - HGNC]
DOCK6:dedicator of cytokinesis 6 [Gene - OMIM - HGNC]
DHPS:deoxyhypusine synthase [Gene - OMIM - HGNC]
DNASE2:deoxyribonuclease 2, lysosomal [Gene - OMIM - HGNC]
DNM2:dynamin 2 [Gene - OMIM - HGNC]
ELOF1:elongation factor 1 [Gene - OMIM - HGNC]
EPOR:erythropoietin receptor [Gene - OMIM - HGNC]
GCDH:glutaryl-CoA dehydrogenase [Gene - OMIM - HGNC]
GET3:guided entry of tail-anchored proteins factor 3, ATPase [Gene - OMIM - HGNC]
HOOK2:hook microtubule tethering protein 2 [Gene - OMIM - HGNC]
IER2:immediate early response 2 [Gene - OMIM - HGNC]
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
MAN2B1:mannosidase alpha class 2B member 1 [Gene - OMIM - HGNC]
MIR199A1:microRNA 199a-1 [Gene - OMIM - HGNC]
MAST1:microtubule associated serine/threonine kinase 1 [Gene - OMIM - HGNC]
NFIX:nuclear factor I X [Gene - OMIM - HGNC]
NACC1:nucleus accumbens associated 1 [Gene - OMIM - HGNC]
ODAD3:outer dynein arm docking complex subunit 3 [Gene - OMIM - HGNC]
PRDX2:peroxiredoxin 2 [Gene - OMIM - HGNC]
FARSA:phenylalanyl-tRNA synthetase subunit alpha [Gene - OMIM - HGNC]
PRKCSH:protein kinase C substrate 80K-H [Gene - OMIM - HGNC]
RGL3:ral guanine nucleotide dissociation stimulator like 3 [Gene - OMIM - HGNC]
RTBDN:retbindin [Gene - OMIM - HGNC]
RNASEH2A:ribonuclease H2 subunit A [Gene - OMIM - HGNC]
SYCE2:synaptonemal complex central element protein 2 [Gene - OMIM - HGNC]
STX10:syntaxin 10 [Gene - OMIM - HGNC]
TRMT1:tRNA methyltransferase 1 [Gene - OMIM - HGNC]
TRIR:telomerase RNA component interacting RNase [Gene - HGNC]
TSPAN16:tetraspanin 16 [Gene - OMIM - HGNC]
TIMM29:translocase of inner mitochondrial membrane 29 [Gene - OMIM - HGNC]
TMED1:transmembrane p24 trafficking protein 1 [Gene - OMIM - HGNC]
TMEM205:transmembrane protein 205 [Gene - OMIM - HGNC]
TNPO2:transportin 2 [Gene - OMIM - HGNC]
ZNF136:zinc finger protein 136 [Gene - OMIM - HGNC]
ZNF20:zinc finger protein 20 [Gene - OMIM - HGNC]
ZNF433:zinc finger protein 433 [Gene - HGNC]
ZNF439:zinc finger protein 439 [Gene - HGNC]
ZNF440:zinc finger protein 440 [Gene - HGNC]
ZNF441:zinc finger protein 441 [Gene - HGNC]
ZNF442:zinc finger protein 442 [Gene - HGNC]
ZNF443:zinc finger protein 443 [Gene - OMIM - HGNC]
ZNF44:zinc finger protein 44 [Gene - OMIM - HGNC]
ZNF490:zinc finger protein 490 [Gene - OMIM - HGNC]
ZNF491:zinc finger protein 491 [Gene - HGNC]
ZNF563:zinc finger protein 563 [Gene - HGNC]
ZNF564:zinc finger protein 564 [Gene - HGNC]
ZNF625:zinc finger protein 625 [Gene - HGNC]
ZNF627:zinc finger protein 627 [Gene - OMIM - HGNC]
ZNF653:zinc finger protein 653 [Gene - OMIM - HGNC]
ZNF69:zinc finger protein 69 [Gene - OMIM - HGNC]
ZNF700:zinc finger protein 700 [Gene - HGNC]
ZNF709:zinc finger protein 709 [Gene - HGNC]
ZNF763:zinc finger protein 763 [Gene - HGNC]
ZNF791:zinc finger protein 791 [Gene - HGNC]
ZNF799:zinc finger protein 799 [Gene - OMIM - HGNC]
ZNF823:zinc finger protein 823 [Gene - HGNC]
ZNF844:zinc finger protein 844 [Gene - HGNC]
ZNF878:zinc finger protein 878 [Gene - HGNC]

Variant type:

Duplication

Cytogenetic location:

19p13.2

Genomic location:

Chr19: 10828919 - 13482613 (on Assembly GRCh37)

Preferred name:

NC_000019.9:g.(?_10828919)_(13482613_?)dup

HGVS:

NC_000019.9:g.(?_10828919)_(13482613_?)dup

Condition(s)

Name:: Episodic ataxia type 2 (EA2)
Synonyms:: Episodic ataxia with nystagmus; Nystagmus-associated episodic ataxia; Cerebellopathy, hereditary paroxysmal; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007163; MedGen: C1720416; Orphanet: 97; OMIM: 108500

Name:: Developmental and epileptic encephalopathy, 42 (DEE42)
Synonyms:: Epileptic encephalopathy, early infantile, 42
Identifiers:: MONDO: MONDO:0014917; MedGen: C4310716; OMIM: 617106

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003792254	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 6, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003792254

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 6, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003792254.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant results in a copy number gain of the genomic region encompassing exon(s) 4-47 of the CACNA1A gene. This region includes the termination codon of the gene. This copy number gain extends 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. This variant has not been reported in the literature in individuals affected with CACNA1A-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 5, 2023

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