GRCh37/hg19 9q21.33-22.2(chr9:90342469-93657932)x1 AND See cases

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 23, 2021
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:: RCV003329413.3

Allele description [Variation Report for GRCh37/hg19 9q21.33-22.2(chr9:90342469-93657932)x1]

GRCh37/hg19 9q21.33-22.2(chr9:90342469-93657932)x1

Genes:

CKS2:CDC28 protein kinase regulatory subunit 2 [Gene - OMIM - HGNC]
DIRAS2:DIRAS family GTPase 2 [Gene - OMIM - HGNC]
SECISBP2:SECIS binding protein 2 [Gene - OMIM - HGNC]
SHC3:SHC adaptor protein 3 [Gene - OMIM - HGNC]
SPATA31C1:SPATA31 subfamily C member 1 [Gene - HGNC]
SPATA31C2:SPATA31 subfamily C member 2 [Gene - HGNC]
SPATA31E1:SPATA31 subfamily E member 1 [Gene - HGNC]
CTSL:cathepsin L [Gene - OMIM - HGNC]
C9orf47:chromosome 9 open reading frame 47 [Gene - HGNC]
CDK20:cyclin dependent kinase 20 [Gene - OMIM - HGNC]
GADD45G:growth arrest and DNA damage inducible gamma [Gene - OMIM - HGNC]
NXNL2:nucleoredoxin like 2 [Gene - OMIM - HGNC]
SEMA4D:semaphorin 4D [Gene - OMIM - HGNC]
S1PR3:sphingosine-1-phosphate receptor 3 [Gene - OMIM - HGNC]
SPIN1:spindlin 1 [Gene - OMIM - HGNC]
SYK:spleen associated tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

9q21.33-22.2

Genomic location:

Chr9: 90342469 - 93657932 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 9q21.33-22.2(chr9:90342469-93657932)x1

HGVS:

NC_000009.11:g.(?_90342469)_(93657932_?)del

Condition(s)

Name:: See cases [See the Variation display for details]
Identifiers:

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Leucine Rich repeat-containing domain protein [Caenorhabditis elegans]
Leucine Rich repeat-containing domain protein [Caenorhabditis elegans]
gi|1767231820|ref|NP_001361867.1|

Protein
charged multivesicular body protein 7 isoform X2 [Homo sapiens]
charged multivesicular body protein 7 isoform X2 [Homo sapiens]
gi|2462621615|ref|XP_054217474.1|

Protein
exosome complex component CSL4 isoform X2 [Phascolarctos cinereus]
exosome complex component CSL4 isoform X2 [Phascolarctos cinereus]
gi|1190405212|ref|XP_020852767.1|

Protein
Vapb VAMP associated protein B and C [Rattus norvegicus]
Vapb VAMP associated protein B and C [Rattus norvegicus]
Gene ID:60431

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002047401	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Likely pathogenic (Jul 23, 2021)	de novo	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

SCV002047401

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Likely pathogenic
(Jul 23, 2021)

de novo

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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Institute of Human Genetics, University of Leipzig Medical Center, SCV002047401.1

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

#	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		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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