Single allele AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 1, 2023
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:: RCV003448669.1

Allele description [Variation Report for Single allele]

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]
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]
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:

Deletion

Cytogenetic location:

5q35.2-35.3

Genomic location:

Chr5: 175559209 - 177430432 (on Assembly GRCh37)

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Human DNA sequence from clone ICI-21GA2 on chromosome 9, complete sequence
Human DNA sequence from clone ICI-21GA2 on chromosome 9, complete sequence
gi|29603317|emb|AL772337.17|

Nucleotide
DUF2922 domain-containing protein [Lactobacillus sp. DS2_6]
DUF2922 domain-containing protein [Lactobacillus sp. DS2_6]
gi|1377336706|gb|PTS54670.1||gnl|WG U|DBQ60_01245

Protein
hypothetical protein DBQ60_01250 [Lactobacillus sp. DS2_6]
hypothetical protein DBQ60_01250 [Lactobacillus sp. DS2_6]
gi|1377336707|gb|PTS54671.1||gnl|WG U|DBQ60_01250

Protein
DA786334 OCBBF2 Homo sapiens cDNA clone OCBBF2023387 5', mRNA sequence
DA786334 OCBBF2 Homo sapiens cDNA clone OCBBF2023387 5', mRNA sequence
gi|82359280|gnl|dbEST|33818561|dbj| 334.1|

Nucleotide
Human chromosome 14 DNA sequence BAC C-2588C21 of library CalTech-D from chromos...
Human chromosome 14 DNA sequence BAC C-2588C21 of library CalTech-D from chromosome 14 of Homo sapiens (Human), complete sequence
gi|17154410|emb|AL138539.7|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004176311	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL CNVClassificationCriteria Aug2020)	Pathogenic (Sep 1, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004176311

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL CNVClassificationCriteria Aug2020)

Pathogenic
(Sep 1, 2023)

unknown

clinical testing

Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV004176311.1

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

Description

This CNV is a 1.87 Mb deletion of 5q35.2q35.3 on chromosome 5, (seq[GRCh37]del(5)(q35.2q35.3);NC_000005.9:g.175559209_ 177430432del), that occurred de novo. This event is located near the q terminus of chromosome 5 but does not extend to the telomere. This CNV encompasses 38 protein coding genes, including NSD1, DDX41, and SLC34A1. Haploinsufficiency of NSD1 is a known cause of Sotos syndrome (PMID: 11896389; 17565729; 20301652; 23190751). Microdeletions of 5q35.2q35.3 involving NSD1 have been especially frequently observed in Japanese patients with Sotos syndrome (PMID: 14517949; 20301652). Similar CNVs have not been reported in controls (PMID: 21841781; 24174537). This CNV also encompasses the DDX41 gene, haploinsufficiency of which is associated with DDX41-related hematologic malignancy predisposition syndrome. Based on the available evidence, this CNV is classified as pathogenic.

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

Last Updated: Dec 17, 2023

ClinVar

Relating variation to medicine