NC_000005.9:g.(?_175158654)_(179263593_?)dup AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 3, 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:: RCV003154288.8

Allele description

NC_000005.9:g.(?_175158654)_(179263593_?)dup

Genes:

PHYKPL:5-phosphohydroxy-L-lysine phospho-lyase [Gene - OMIM - HGNC]
ADAMTS2:ADAM metallopeptidase with thrombospondin type 1 motif 2 [Gene - OMIM - HGNC]
ARL10:ADP ribosylation factor like GTPase 10 [Gene - HGNC]
CLK4:CDC like kinase 4 [Gene - OMIM - HGNC]
DDX41:DEAD-box helicase 41 [Gene - OMIM - HGNC]
FAF2:Fas associated factor family member 2 [Gene - OMIM - HGNC]
GPRIN1:G protein regulated inducer of neurite outgrowth 1 [Gene - OMIM - HGNC]
GRK6:G protein-coupled receptor kinase 6 [Gene - OMIM - HGNC]
HIGD2A:HIG1 hypoxia inducible domain family member 2A [Gene - OMIM - HGNC]
KIAA1191:KIAA1191 [Gene - HGNC]
MXD3:MAX dimerization protein 3 [Gene - OMIM - HGNC]
N4BP3:NEDD4 binding protein 3 [Gene - OMIM - HGNC]
NHP2:NHP2 ribonucleoprotein [Gene - OMIM - HGNC]
NOP16:NOP16 nucleolar protein [Gene - OMIM - HGNC]
PDLIM7:PDZ and LIM domain 7 [Gene - OMIM - HGNC]
PRELID1:PRELI domain containing 1 [Gene - OMIM - HGNC]
PROP1:PROP paired-like homeobox 1 [Gene - OMIM - HGNC]
RAB24:RAB24, member RAS oncogene family [Gene - OMIM - HGNC]
RUFY1:RUN and FYVE domain containing 1 [Gene - OMIM - HGNC]
SPATA31J1:SPATA31 subfamily J member 1 [Gene - HGNC]
SIMC1:SUMO interacting motifs containing 1 [Gene - OMIM - HGNC]
THOC3:THO complex subunit 3 [Gene - OMIM - HGNC]
ZFP2:ZFP2 zinc finger protein [Gene - HGNC]
MGAT4B:alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B [Gene - OMIM - HGNC]
B4GALT7:beta-1,4-galactosyltransferase 7 [Gene - OMIM - HGNC]
CDHR2:cadherin related family member 2 [Gene - OMIM - HGNC]
CANX:calnexin [Gene - OMIM - HGNC]
CBY3:chibby family member 3 [Gene - OMIM - HGNC]
CLTB:clathrin light chain B [Gene - OMIM - HGNC]
F12:coagulation factor XII [Gene - OMIM - HGNC]
COL23A1:collagen type XXIII alpha 1 chain [Gene - OMIM - HGNC]
CPLX2:complexin 2 [Gene - OMIM - HGNC]
DOK3:docking protein 3 [Gene - OMIM - HGNC]
DBN1:drebrin 1 [Gene - OMIM - HGNC]
EIF4E1B:eukaryotic translation initiation factor 4E family member 1B [Gene - HGNC]
FAM153A:family with sequence similarity 153 member A [Gene - HGNC]
FAM153B:family with sequence similarity 153 member B [Gene - HGNC]
FAM193B:family with sequence similarity 193 member B [Gene - OMIM - HGNC]
FGFR4:fibroblast growth factor receptor 4 [Gene - OMIM - HGNC]
GRM6:glutamate metabotropic receptor 6 [Gene - OMIM - HGNC]
HNRNPAB:heterogeneous nuclear ribonucleoprotein A/B [Gene - OMIM - HGNC]
HNRNPH1:heterogeneous nuclear ribonucleoprotein H1 [Gene - OMIM - HGNC]
HK3:hexokinase 3 [Gene - OMIM - HGNC]
LMAN2:lectin, mannose binding 2 [Gene - OMIM - HGNC]
LTC4S:leukotriene C4 synthase [Gene - OMIM - HGNC]
MAML1:mastermind like transcriptional coactivator 1 [Gene - OMIM - HGNC]
NSD1:nuclear receptor binding SET domain protein 1 [Gene - OMIM - HGNC]
PFN3:profilin 3 [Gene - OMIM - HGNC]
PRR7:proline rich 7, synaptic [Gene - OMIM - HGNC]
RGS14:regulator of G protein signaling 14 [Gene - OMIM - HGNC]
RMND5B:required for meiotic nuclear division 5 homolog B [Gene - HGNC]
RNF44:ring finger protein 44 [Gene - OMIM - HGNC]
SQSTM1:sequestosome 1 [Gene - OMIM - HGNC]
SLC34A1:solute carrier family 34 member 1 [Gene - OMIM - HGNC]
SNCB:synuclein beta [Gene - OMIM - HGNC]
TSPAN17:tetraspanin 17 [Gene - OMIM - HGNC]
TMED9:transmembrane p24 trafficking protein 9 [Gene - OMIM - HGNC]
UIMC1:ubiquitin interaction motif containing 1 [Gene - OMIM - HGNC]
UNC5A:unc-5 netrin receptor A [Gene - OMIM - HGNC]
ZNF346:zinc finger protein 346 [Gene - OMIM - HGNC]
ZNF354A:zinc finger protein 354A [Gene - OMIM - HGNC]
ZNF354B:zinc finger protein 354B [Gene - HGNC]
ZNF354C:zinc finger protein 354C [Gene - OMIM - HGNC]
ZNF454:zinc finger protein 454 [Gene - HGNC]
ZNF879:zinc finger protein 879 [Gene - HGNC]

Variant type:

Duplication

Cytogenetic location:

5q35.2-35.3

Genomic location:

Chr5: 175158654 - 179263593 (on Assembly GRCh37)

Preferred name:

NC_000005.9:g.(?_175158654)_(179263593_?)dup

HGVS:

NC_000005.9:g.(?_175158654)_(179263593_?)dup

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003843969	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 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

SCV003843969

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 3, 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, SCV003843969.1

#	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 DDX41 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 DDX41-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: Sep 16, 2024

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