GRCh37/hg19 5q35.2-35.3(chr5:175346695-177469711)x1 AND Sotos syndrome

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 3, 2020
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV003232270.6

Allele description

GRCh37/hg19 5q35.2-35.3(chr5:175346695-177469711)x1

Genes:

ARL10:ADP ribosylation factor like GTPase 10 [Gene - 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 - HGNC]
KIAA1191:KIAA1191 [Gene - HGNC]
MXD3:MAX dimerization protein 3 [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]
SIMC1:SUMO interacting motifs containing 1 [Gene - OMIM - HGNC]
THOC3:THO complex subunit 3 [Gene - OMIM - HGNC]
B4GALT7:beta-1,4-galactosyltransferase 7 [Gene - OMIM - HGNC]
CDHR2:cadherin related family member 2 [Gene - OMIM - HGNC]
CLTB:clathrin light chain B [Gene - OMIM - HGNC]
F12:coagulation factor XII [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]
HK3:hexokinase 3 [Gene - OMIM - HGNC]
LMAN2:lectin, mannose binding 2 [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]
RNF44:ring finger protein 44 [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]

Variant type:

copy number loss

Cytogenetic location:

5q35.2-35.3

Genomic location:

Chr5: 175346695 - 177469711 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 5q35.2-35.3(chr5:175346695-177469711)x1

HGVS:

NC_000005.9:g.(?_175346695)_(177469711_?)del

Observations:

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:: MedGen: C0175695; Orphanet: 821; OMIM: 117550

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001370536	Molecular Genetics Laboratory Heidelberg, Heidelberg University	no assertion criteria provided	Pathogenic (Jul 3, 2020)	de novo	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001370536

Molecular Genetics Laboratory Heidelberg, Heidelberg University

no assertion criteria provided

Pathogenic
(Jul 3, 2020)

de novo

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Molecular Genetics Laboratory Heidelberg, Heidelberg University, SCV001370536.1

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

Description

Genomic copy number losses including NSD1 are a well known cause of Sotos syndrome. The copy number loss occurred the novo and it is absent from controls (database dgv).

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

Last Updated: Sep 30, 2023

ClinVar

Relating variation to medicine