NC_000012.11:g.(?_4368352)_(9027607_?)dup AND Lymphoproliferative syndrome 2

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 30, 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:: RCV003105682.2

Allele description

NC_000012.11:g.(?_4368352)_(9027607_?)dup

Genes:

AKAP3:A-kinase anchoring protein 3 [Gene - OMIM - HGNC]
CLEC6A:C-type lectin domain containing 6A [Gene - OMIM - HGNC]
CLEC4A:C-type lectin domain family 4 member A [Gene - OMIM - HGNC]
CLEC4C:C-type lectin domain family 4 member C [Gene - OMIM - HGNC]
CLEC4D:C-type lectin domain family 4 member D [Gene - OMIM - HGNC]
CLEC4E:C-type lectin domain family 4 member E [Gene - OMIM - HGNC]
CD163L1:CD163 molecule like 1 [Gene - OMIM - HGNC]
CD163:CD163 molecule [Gene - OMIM - HGNC]
CD27:CD27 molecule [Gene - OMIM - HGNC]
CD4:CD4 molecule [Gene - OMIM - HGNC]
CD9:CD9 molecule [Gene - OMIM - HGNC]
COPS7A:COP9 signalosome subunit 7A [Gene - OMIM - HGNC]
EMG1:EMG1 N1-specific pseudouridine methyltransferase [Gene - OMIM - HGNC]
GNB3:G protein subunit beta 3 [Gene - OMIM - HGNC]
GPR162:G protein-coupled receptor 162 [Gene - HGNC]
NDUFA9:NADH:ubiquinone oxidoreductase subunit A9 [Gene - OMIM - HGNC]
NANOGNB:NANOG neighbor homeobox [Gene - HGNC]
NECAP1:NECAP endocytosis associated 1 [Gene - OMIM - HGNC]
NOP2:NOP2 nucleolar protein [Gene - OMIM - HGNC]
NANOG:Nanog homeobox [Gene - OMIM - HGNC]
PIANP:PILR alpha associated neural protein [Gene - OMIM - HGNC]
RAD51AP1:RAD51 associated protein 1 [Gene - OMIM - HGNC]
TAPBPL:TAP binding protein like [Gene - OMIM - HGNC]
TNFRSF1A:TNF receptor superfamily member 1A [Gene - OMIM - HGNC]
TIGAR:TP53 induced glycolysis regulatory phosphatase [Gene - OMIM - HGNC]
ACRBP:acrosin binding protein [Gene - OMIM - HGNC]
AICDA:activation induced cytidine deaminase [Gene - OMIM - HGNC]
ACSM4:acyl-CoA synthetase medium chain family member 4 [Gene - OMIM - HGNC]
A2ML1:alpha-2-macroglobulin like 1 [Gene - OMIM - HGNC]
ANO2:anoctamin 2 [Gene - OMIM - HGNC]
APOBEC1:apolipoprotein B mRNA editing enzyme catalytic subunit 1 [Gene - OMIM - HGNC]
ATN1:atrophin 1 [Gene - OMIM - HGNC]
CLSTN3:calsyntenin 3 [Gene - OMIM - HGNC]
CDCA3:cell division cycle associated 3 [Gene - OMIM - HGNC]
CHD4:chromodomain helicase DNA binding protein 4 [Gene - OMIM - HGNC]
C12orf4:chromosome 12 open reading frame 4 [Gene - OMIM - HGNC]
C12orf57:chromosome 12 open reading frame 57 [Gene - OMIM - HGNC]
C1RL:complement C1r subcomponent like [Gene - OMIM - HGNC]
C1R:complement C1r [Gene - OMIM - HGNC]
C1S:complement C1s [Gene - OMIM - HGNC]
C3AR1:complement C3a receptor 1 [Gene - OMIM - HGNC]
CCND2:cyclin D2 [Gene - OMIM - HGNC]
DPPA3:developmental pluripotency associated 3 [Gene - OMIM - HGNC]
DYRK4:dual specificity tyrosine phosphorylation regulated kinase 4 [Gene - OMIM - HGNC]
ENO2:enolase 2 [Gene - OMIM - HGNC]
FAM90A1:family with sequence similarity 90 member A1 [Gene - OMIM - HGNC]
FGF23:fibroblast growth factor 23 [Gene - OMIM - HGNC]
FGF6:fibroblast growth factor 6 [Gene - OMIM - HGNC]
FOXJ2:forkhead box J2 [Gene - OMIM - HGNC]
GAPDH:glyceraldehyde-3-phosphate dehydrogenase [Gene - OMIM - HGNC]
GDF3:growth differentiation factor 3 [Gene - OMIM - HGNC]
ING4:inhibitor of growth family member 4 [Gene - OMIM - HGNC]
IFFO1:intermediate filament family orphan 1 [Gene - OMIM - HGNC]
LRRC23:leucine rich repeat containing 23 [Gene - HGNC]
LAG3:lymphocyte activating 3 [Gene - OMIM - HGNC]
LTBR:lymphotoxin beta receptor [Gene - OMIM - HGNC]
LPAR5:lysophosphatidic acid receptor 5 [Gene - OMIM - HGNC]
LPCAT3:lysophosphatidylcholine acyltransferase 3 [Gene - OMIM - HGNC]
MIR141:microRNA 141 [Gene - OMIM - HGNC]
MIR200C:microRNA 200c [Gene - OMIM - HGNC]
MFAP5:microfibril associated protein 5 [Gene - OMIM - HGNC]
MRPL51:mitochondrial ribosomal protein L51 [Gene - OMIM - HGNC]
MLF2:myeloid leukemia factor 2 [Gene - OMIM - HGNC]
NTF3:neurotrophin 3 [Gene - OMIM - HGNC]
NCAPD2:non-SMC condensin I complex subunit D2 [Gene - OMIM - HGNC]
PTMS:parathymosin [Gene - OMIM - HGNC]
PEX5:peroxisomal biogenesis factor 5 [Gene - OMIM - HGNC]
PLEKHG6:pleckstrin homology and RhoGEF domain containing G6 [Gene - OMIM - HGNC]
GALNT8:polypeptide N-acetylgalactosaminyltransferase 8 [Gene - OMIM - HGNC]
KCNA1:potassium voltage-gated channel subfamily A member 1 [Gene - OMIM - HGNC]
KCNA5:potassium voltage-gated channel subfamily A member 5 [Gene - OMIM - HGNC]
KCNA6:potassium voltage-gated channel subfamily A member 6 [Gene - OMIM - HGNC]
PHB2:prohibitin 2 [Gene - OMIM - HGNC]
P3H3:prolyl 3-hydroxylase 3 [Gene - OMIM - HGNC]
PTPN6:protein tyrosine phosphatase non-receptor type 6 [Gene - OMIM - HGNC]
RBP5:retinol binding protein 5 [Gene - OMIM - HGNC]
RIMKLB:ribosomal modification protein rimK like family member B [Gene - OMIM - HGNC]
SCNN1A:sodium channel epithelial 1 subunit alpha [Gene - OMIM - HGNC]
SLC2A14:solute carrier family 2 member 14 [Gene - OMIM - HGNC]
SLC2A3:solute carrier family 2 member 3 [Gene - OMIM - HGNC]
SPSB2:splA/ryanodine receptor domain and SOCS box containing 2 [Gene - OMIM - HGNC]
TPI1:triosephosphate isomerase 1 [Gene - OMIM - HGNC]
USP5:ubiquitin specific peptidase 5 [Gene - OMIM - HGNC]
VAMP1:vesicle associated membrane protein 1 [Gene - OMIM - HGNC]
VWF:von Willebrand factor [Gene - OMIM - HGNC]
ZNF384:zinc finger protein 384 [Gene - OMIM - HGNC]
ZNF705A:zinc finger protein 705A [Gene - HGNC]

Variant type:

Duplication

Cytogenetic location:

12p13.32-13.31

Genomic location:

Chr12: 4368352 - 9027607 (on Assembly GRCh37)

Preferred name:

NC_000012.11:g.(?_4368352)_(9027607_?)dup

HGVS:

NC_000012.11:g.(?_4368352)_(9027607_?)dup

Condition(s)

Name:: Lymphoproliferative syndrome 2 (LPFS2)
Synonyms:: CD27 DEFICIENCY
Identifiers:: MONDO: MONDO:0014054; MedGen: C3554540; Orphanet: 238505; OMIM: 615122

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003793394	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 30, 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

SCV003793394

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 30, 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, SCV003793394.1

#	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 CD27 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 CD27-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

Last Updated: Mar 26, 2023

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