NC_000001.10:g.(?_200522516)_(208391267_?)dup AND multiple conditions

Germline classification:: no classifications from unflagged records (1 submission)
Review status:: no classifications from unflagged records

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:: RCV003119239.5

Allele description [Variation Report for NC_000001.10:g.(?_200522516)_(208391267_?)dup]

NC_000001.10:g.(?_200522516)_(208391267_?)dup

Genes:

PFKFB2:6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 [Gene - OMIM - HGNC]
ARL8A:ADP ribosylation factor like GTPase 8A [Gene - OMIM - HGNC]
ATP2B4:ATPase plasma membrane Ca2+ transporting 4 [Gene - OMIM - HGNC]
BTG2:BTG anti-proliferation factor 2 [Gene - OMIM - HGNC]
CD34:CD34 molecule [Gene - OMIM - HGNC]
CD46:CD46 molecule [Gene - OMIM - HGNC]
CD55:CD55 molecule (Cromer blood group) [Gene - OMIM - HGNC]
DDX59:DEAD-box helicase 59 [Gene - OMIM - HGNC]
ELF3:E74 like ETS transcription factor 3 [Gene - OMIM - HGNC]
ELK4:ETS transcription factor ELK4 [Gene - OMIM - HGNC]
FCAMR:Fc alpha and mu receptor [Gene - OMIM - HGNC]
FCMR:Fc mu receptor [Gene - OMIM - HGNC]
GPR25:G protein-coupled receptor 25 [Gene - OMIM - HGNC]
GPR37L1:G protein-coupled receptor 37 like 1 [Gene - OMIM - HGNC]
IKBKE-AS1:IKBKE antisense RNA 1 [Gene - HGNC]
KISS1:KiSS-1 metastasis suppressor [Gene - OMIM - HGNC]
LEMD1:LEM domain containing 1 [Gene - OMIM - HGNC]
MAPKAPK2:MAPK activated protein kinase 2 [Gene - OMIM - HGNC]
MDM4:MDM4 regulator of p53 [Gene - OMIM - HGNC]
MIR29B2CHG:MIR29B2 and MIR29C host gene [Gene - HGNC]
NUAK2:NUAK family kinase 2 [Gene - OMIM - HGNC]
PPFIA4:PTPRF interacting protein alpha 4 [Gene - OMIM - HGNC]
RABIF:RAB interacting factor [Gene - OMIM - HGNC]
RAB29:RAB29, member RAS oncogene family [Gene - OMIM - HGNC]
RBBP5:RB binding protein 5, histone lysine methyltransferase complex subunit [Gene - OMIM - HGNC]
RASSF5:Ras association domain family member 5 [Gene - OMIM - HGNC]
SRGAP2:SLIT-ROBO Rho GTPase activating protein 2 [Gene - OMIM - HGNC]
SOX13:SRY-box transcription factor 13 [Gene - OMIM - HGNC]
YOD1:YOD1 deubiquitinase [Gene - OMIM - HGNC]
ASCL5:achaete-scute family bHLH transcription factor 5 [Gene - HGNC]
ADORA1:adenosine A1 receptor [Gene - OMIM - HGNC]
ADIPOR1:adiponectin receptor 1 [Gene - OMIM - HGNC]
AVPR1B:arginine vasopressin receptor 1B [Gene - OMIM - HGNC]
RNPEP:arginyl aminopeptidase [Gene - OMIM - HGNC]
CACNA1S:calcium voltage-gated channel subunit alpha1 S [Gene - OMIM - HGNC]
CAMSAP2:calmodulin regulated spectrin associated protein family member 2 [Gene - OMIM - HGNC]
CTSE:cathepsin E [Gene - OMIM - HGNC]
CHIT1:chitinase 1 [Gene - OMIM - HGNC]
CHI3L1:chitinase 3 like 1 [Gene - OMIM - HGNC]
C1orf116:chromosome 1 open reading frame 116 [Gene - OMIM - HGNC]
CR1:complement C3b/C4b receptor 1 (Knops blood group) [Gene - OMIM - HGNC]
CR1L:complement C3b/C4b receptor 1 like [Gene - OMIM - HGNC]
CR2:complement C3d receptor 2 [Gene - OMIM - HGNC]
C4BPA:complement component 4 binding protein alpha [Gene - OMIM - HGNC]
C4BPB:complement component 4 binding protein beta [Gene - OMIM - HGNC]
CNTN2:contactin 2 [Gene - OMIM - HGNC]
CDK18:cyclin dependent kinase 18 [Gene - OMIM - HGNC]
CSRP1:cysteine and glycine rich protein 1 [Gene - OMIM - HGNC]
CYB5R1:cytochrome b5 reductase 1 [Gene - OMIM - HGNC]
DSTYK:dual serine/threonine and tyrosine protein kinase [Gene - OMIM - HGNC]
DYRK3:dual specificity tyrosine phosphorylation regulated kinase 3 [Gene - OMIM - HGNC]
ETNK2:ethanolamine kinase 2 [Gene - OMIM - HGNC]
EIF2D:eukaryotic translation initiation factor 2D [Gene - OMIM - HGNC]
FAM72A:family with sequence similarity 72 member A [Gene - OMIM - HGNC]
FMOD:fibromodulin [Gene - OMIM - HGNC]
GOLT1A:golgi transport 1A [Gene - OMIM - HGNC]
IGFN1:immunoglobulin like and fibronectin type III domain containing 1 [Gene - OMIM - HGNC]
IPO9:importin 9 [Gene - HGNC]
IKBKE:inhibitor of nuclear factor kappa B kinase subunit epsilon [Gene - OMIM - HGNC]
INAVA:innate immunity activator [Gene - OMIM - HGNC]
IL10:interleukin 10 [Gene - OMIM - HGNC]
IL19:interleukin 19 [Gene - OMIM - HGNC]
IL20:interleukin 20 [Gene - OMIM - HGNC]
IL24:interleukin 24 [Gene - OMIM - HGNC]
KLHDC8A:kelch domain containing 8A [Gene - OMIM - HGNC]
KLHL12:kelch like family member 12 [Gene - OMIM - HGNC]
KIF14:kinesin family member 14 [Gene - OMIM - HGNC]
KIF21B:kinesin family member 21B [Gene - OMIM - HGNC]
LAD1:ladinin 1 [Gene - OMIM - HGNC]
LMOD1:leiomodin 1 [Gene - OMIM - HGNC]
LGR6:leucine rich repeat containing G protein-coupled receptor 6 [Gene - OMIM - HGNC]
LRRN2:leucine rich repeat neuronal 2 [Gene - OMIM - HGNC]
LAX1:lymphocyte transmembrane adaptor 1 [Gene - OMIM - HGNC]
KDM5B:lysine demethylase 5B [Gene - OMIM - HGNC]
MFSD4A:major facilitator superfamily domain containing 4A [Gene - OMIM - HGNC]
MIR29C:microRNA 29c [Gene - OMIM - HGNC]
MYOG:myogenin [Gene - OMIM - HGNC]
MYBPH:myosin binding protein H [Gene - OMIM - HGNC]
NFASC:neurofascin [Gene - OMIM - HGNC]
NAV1:neuron navigator 1 [Gene - OMIM - HGNC]
NUCKS1:nuclear casein kinase and cyclin dependent kinase substrate 1 [Gene - OMIM - HGNC]
OPTC:opticin [Gene - OMIM - HGNC]
PM20D1:peptidase M20 domain containing 1 [Gene - OMIM - HGNC]
PIK3C2B:phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta [Gene - OMIM - HGNC]
PKP1:plakophilin 1 [Gene - OMIM - HGNC]
PLEKHA6:pleckstrin homology domain containing A6 [Gene - OMIM - HGNC]
PHLDA3:pleckstrin homology like domain family A member 3 [Gene - OMIM - HGNC]
PLXNA2:plexin A2 [Gene - OMIM - HGNC]
PIGR:polymeric immunoglobulin receptor [Gene - OMIM - HGNC]
PRELP:proline and arginine rich end leucine rich repeat protein [Gene - OMIM - HGNC]
PCAT6:prostate cancer associated transcript 6 [Gene - HGNC]
PPP1R12B:protein phosphatase 1 regulatory subunit 12B [Gene - OMIM - HGNC]
PPP1R15B:protein phosphatase 1 regulatory subunit 15B [Gene - OMIM - HGNC]
PTPN7:protein tyrosine phosphatase non-receptor type 7 [Gene - OMIM - HGNC]
RHEX:regulator of hemoglobinization and erythroid cell expansion [Gene - OMIM - HGNC]
REN:renin [Gene - OMIM - HGNC]
SHISA4:shisa family member 4 [Gene - OMIM - HGNC]
SNRPE:small nuclear ribonucleoprotein polypeptide E [Gene - OMIM - HGNC]
SLC26A9:solute carrier family 26 member 9 [Gene - OMIM - HGNC]
SLC41A1:solute carrier family 41 member 1 [Gene - OMIM - HGNC]
SLC45A3:solute carrier family 45 member 3 [Gene - OMIM - HGNC]
SYT2:synaptotagmin 2 [Gene - OMIM - HGNC]
TIMM17A:translocase of inner mitochondrial membrane 17A [Gene - OMIM - HGNC]
TMCC2:transmembrane and coiled-coil domain family 2 [Gene - OMIM - HGNC]
TMEM183A:transmembrane protein 183A [Gene - HGNC]
TMEM81:transmembrane protein 81 [Gene - HGNC]
TMEM9:transmembrane protein 9 [Gene - OMIM - HGNC]
TNNI1:troponin I1, slow skeletal type [Gene - OMIM - HGNC]
TNNT2:troponin T2, cardiac type [Gene - OMIM - HGNC]
UBE2T:ubiquitin conjugating enzyme E2 T [Gene - OMIM - HGNC]
ZBED6:zinc finger BED-type containing 6 [Gene - OMIM - HGNC]
ZC3H11A:zinc finger CCCH-type containing 11A [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

1q32.1-32.2

Genomic location:

Chr1: 200522516 - 208391267 (on Assembly GRCh37)

Preferred name:

NC_000001.10:g.(?_200522516)_(208391267_?)dup

HGVS:

NC_000001.10:g.(?_200522516)_(208391267_?)dup

Condition(s)

Name:: Hypokalemic periodic paralysis, type 1
Synonyms:: HypoPP
Identifiers:: MONDO: MONDO:0042979; MedGen: C3714580; Orphanet: 681; OMIM: 170400

Name:: Malignant hyperthermia, susceptibility to, 5 (MHS5)
Synonyms:: Malignant hyperthermia susceptibility type 5; Malignant hyperpyrexia susceptibility type 5
Identifiers:: MONDO: MONDO:0011163; MedGen: C1866077; Orphanet: 423; OMIM: 601887

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No clinical assertions found. See "Flagged submissions" below.

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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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003790205.2

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the CACNA1S 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. This variant has not been reported in the literature in individuals affected with CACNA1S-related conditions. 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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003790205	Invitae	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003790205 appears to be redundant with SCV003796974. (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 3, 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

SCV003790205

Invitae

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV003790205 appears to be redundant with SCV003796974.

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 3, 2022)

germline

clinical testing

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

Last Updated: Dec 9, 2023

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