Single allele AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 5, 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:: RCV003448666.1

Allele description [Variation Report for Single allele]

Genes:

PXYLP1:2-phosphoxylose phosphatase 1 [Gene - OMIM - HGNC]
ATP1B3:ATPase Na+/K+ transporting subunit beta 3 [Gene - OMIM - HGNC]
COPB2:COPI coat complex subunit beta 2 [Gene - OMIM - HGNC]
FOXL2NB:FOXL2 neighbor [Gene - HGNC]
FAIM:Fas apoptotic inhibitory molecule [Gene - OMIM - HGNC]
GRK7:G protein-coupled receptor kinase 7 [Gene - OMIM - HGNC]
NME9:NME/NM23 family member 9 [Gene - OMIM - HGNC]
RASA2:RAS p21 protein activator 2 [Gene - OMIM - HGNC]
ARMC8:armadillo repeat containing 8 [Gene - OMIM - HGNC]
CLSTN2:calsyntenin 2 [Gene - OMIM - HGNC]
CEP70:centrosomal protein 70 [Gene - OMIM - HGNC]
ESYT3:extended synaptotagmin 3 [Gene - OMIM - HGNC]
FOXL2:forkhead box L2 [Gene - OMIM - HGNC]
MRPS22:mitochondrial ribosomal protein S22 [Gene - OMIM - HGNC]
MRAS:muscle RAS oncogene homolog [Gene - OMIM - HGNC]
NMNAT3:nicotinamide nucleotide adenylyltransferase 3 [Gene - OMIM - HGNC]
PIK3CB:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta [Gene - OMIM - HGNC]
PRR23A:proline rich 23A [Gene - HGNC]
PRR23B:proline rich 23B [Gene - HGNC]
PRR23C:proline rich 23C [Gene - HGNC]
RBP1:retinol binding protein 1 [Gene - OMIM - HGNC]
RBP2:retinol binding protein 2 [Gene - OMIM - HGNC]
RNF7:ring finger protein 7 [Gene - OMIM - HGNC]
SLC25A36:solute carrier family 25 member 36 [Gene - OMIM - HGNC]
SPSB4:splA/ryanodine receptor domain and SOCS box containing 4 [Gene - OMIM - HGNC]
TFDP2:transcription factor Dp-2 [Gene - OMIM - HGNC]
TRIM42:tripartite motif containing 42 [Gene - OMIM - HGNC]
ZBTB38:zinc finger and BTB domain containing 38 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q22.3-23

Genomic location:

Chr3: 137912620 - 141811656 (on Assembly GRCh37)

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
SCV004176308	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL CNVClassificationCriteria Aug2020)	Pathogenic (Jun 5, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004176308

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL CNVClassificationCriteria Aug2020)

Pathogenic
(Jun 5, 2023)

unknown

clinical testing

Citation Link

Help

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, SCV004176308.1

#	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 3.9 Mb deletion of 3q22.3-q23 on chromosome 3, (seq[GRCh37]del(3)(q22.3q23);NC_000003.11:g.137912620_141811656del) that occurred de novo. This CNV encompasses 28 protein coding genes, including the FOXL2 gene, which is associated with blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES). Additionally, interstitial deletions specifically involving bands 3q22 and 3q23 have been reported in multiple individuals with BPES (PMID: 8291545; 19344873; 20232352; 21934608). This CNV has not been reported in controls. 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

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