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

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:: RCV003232857.10

Allele description [Variation Report for NC_000005.9:g.(?_175158654)_(179263593_?)dup]

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]
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 - HGNC]
C5orf60:chromosome 5 open reading frame 60 [Gene - 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)

Name:: Sotos syndrome (SOTOS)
Synonyms:: Sotos' syndrome; Cerebral gigantism; Distinctive facial appearance, overgrowth in childhood, and learning disabilities or delayed development; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0019349; MedGen: C0175695; Orphanet: 821; OMIM: 117550

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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

Molecular cytogenetic analysis of de novo dup(5)(q35.2q35.3) and review of the literature of pure partial trisomy 5q.

Chen CP, Lin SP, Lin CC, Chen YJ, Chern SR, Li YC, Hsieh LJ, Lee CC, Pan CW, Wang W.

Am J Med Genet A. 2006 Jul 15;140(14):1594-600. Review.

PubMed [citation]

PMID:: 16770806

MLPA analysis for a panel of syndromes with mental retardation reveals imbalances in 5.8% of patients with mental retardation and dysmorphic features, including duplications of the Sotos syndrome and Williams-Beuren syndrome regions.

Kirchhoff M, Bisgaard AM, Bryndorf T, Gerdes T.

Eur J Med Genet. 2007 Jan-Feb;50(1):33-42. Epub 2006 Oct 10.

PubMed [citation]

PMID:: 17090394

See all PubMed Citations (9)

Details of each submission

From Invitae, SCV003791914.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

A copy number gain of the genomic region encompassing the full coding sequence of the NSD1 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. Isolated whole-gene copy number gains of NSD1 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 16770806, 17090394, 21567906, 23599694, 23913520, 24819041, 28128410, 33389145). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that a similar copy number variant affects NSD1 function (PMID: 33389145). 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
SCV003791914	Invitae	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003791914 appears to be redundant with SCV003843969. (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 25, 2022)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 16770806, 17090394, 21567906, 23599694, 23913520, 24819041, 28128410, 33389145, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791914

Invitae

flagged submission

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

Notes: SCV003791914 appears to be redundant with SCV003843969.

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 25, 2022)

germline

clinical testing

PubMed (9)
[See all records that cite these PMIDs]

Last Updated: May 26, 2024

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