NM_001330078.2(NRXN1):c.772+1128_772+1129del AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Mar 26, 2024
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:: RCV001528238.4

Allele description [Variation Report for NM_001330078.2(NRXN1):c.772+1128_772+1129del]

NM_001330078.2(NRXN1):c.772+1128_772+1129del

Gene:

NRXN1:neurexin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_001330078.2(NRXN1):c.772+1128_772+1129del

HGVS:

NC_000002.12:g.51026374_51026375del
NG_011878.1:g.11163_11164del
NM_001135659.1:c.868_869del
NM_001135659.3:c.868_869del
NM_001330077.2:c.772+1128_772+1129del
NM_001330078.2:c.772+1128_772+1129delMANE SELECT
NM_001330079.2:c.772+1128_772+1129del
NM_001330081.2:c.772+1128_772+1129del
NM_001330082.2:c.772+1128_772+1129del
NM_001330083.2:c.772+1128_772+1129del
NM_001330084.2:c.772+1128_772+1129del
NM_001330085.2:c.772+1128_772+1129del
NM_001330086.2:c.772+1128_772+1129del
NM_001330087.2:c.772+1128_772+1129del
NM_001330088.2:c.772+1128_772+1129del
NM_001330089.2:c.772+1128_772+1129del
NM_001330090.2:c.772+1128_772+1129del
NM_001330093.2:c.772+1128_772+1129del
NM_001330094.2:c.772+1128_772+1129del
NM_001330095.2:c.772+1128_772+1129del
NM_001330096.2:c.772+1128_772+1129del
NM_004801.6:c.772+1128_772+1129del
NP_001129131.1:p.Glu290fs
NC_000002.11:g.51253512_51253513del
NM_001135659.2:c.868_869del

Protein change:

E290fs

Links:

dbSNP: rs1558610072

NCBI 1000 Genomes Browser:

rs1558610072

Molecular consequence:

NM_001135659.3:c.868_869del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330077.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330078.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330079.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330081.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330082.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330083.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330084.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330085.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330086.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330087.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330088.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330089.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330090.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330093.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330094.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330095.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_001330096.2:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]
NM_004801.6:c.772+1128_772+1129del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV001739629	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001969026	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely pathogenic	germline	clinical testing
SCV005334251	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 26, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001739629

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus

no assertion criteria provided

Pathogenic

germline

clinical testing

SCV001969026

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Likely pathogenic

germline

clinical testing

SCV005334251

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 26, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001739629.3

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

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001969026.1

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

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

From GeneDx, SCV005334251.1

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31623504)

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

Last Updated: Oct 8, 2024

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