NM_001042492.3(NF1):c.4600C>T (p.Arg1534Ter) AND not provided

Germline classification:: Pathogenic (5 submissions)
Last evaluated:: Sep 1, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000255589.21

Allele description [Variation Report for NM_001042492.3(NF1):c.4600C>T (p.Arg1534Ter)]

NM_001042492.3(NF1):c.4600C>T (p.Arg1534Ter)

Gene:

NF1:neurofibromin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q11.2

Genomic location:

Preferred name:

NM_001042492.3(NF1):c.4600C>T (p.Arg1534Ter)

HGVS:

NC_000017.11:g.31261733C>T
NG_009018.1:g.171757C>T
NM_000267.3:c.4537C>T
NM_001042492.3:c.4600C>TMANE SELECT
NP_000258.1:p.Arg1513Ter
NP_001035957.1:p.Arg1534Ter
NP_001035957.1:p.Arg1534Ter
LRG_214t1:c.4537C>T
LRG_214t2:c.4600C>T
LRG_214:g.171757C>T
LRG_214p1:p.Arg1513Ter
LRG_214p2:p.Arg1534Ter
NC_000017.10:g.29588751C>T
NM_001042492.2:c.4600C>T
NM_001042492.3:c.4600C>T
p.Arg1513*

Protein change:

R1513*

Links:

dbSNP: rs760703505

NCBI 1000 Genomes Browser:

rs760703505

Molecular consequence:

NM_000267.3:c.4537C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001042492.3:c.4600C>T - nonsense - [Sequence Ontology: SO:0001587]

Functional consequence:

protein truncation [Variation Ontology: 0015]

Observations:

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
SCV000322356	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Sep 6, 2022)	germline	clinical testing	Citation Link,
SCV000842891	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Dec 14, 2017)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 14722917, 16941471, 17209131, 17551851, 17914445, 9180088, 25240281, 26467025
SCV002568857	Laboratoire de Génétique Moléculaire, CHU Bordeaux	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004026311	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 23, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004041991	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Sep 1, 2023)	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	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Characterization of the somatic mutational spectrum of the neurofibromatosis type 1 (NF1) gene in neurofibromatosis patients with benign and malignant tumors.

Upadhyaya M, Han S, Consoli C, Majounie E, Horan M, Thomas NS, Potts C, Griffiths S, Ruggieri M, von Deimling A, Cooper DN.

Hum Mutat. 2004 Feb;23(2):134-146. doi: 10.1002/humu.10305.

PubMed [citation]

PMID:: 14722917

Comprehensive NF1 screening on cultured Schwann cells from neurofibromas.

Maertens O, Brems H, Vandesompele J, De Raedt T, Heyns I, Rosenbaum T, De Schepper S, De Paepe A, Mortier G, Janssens S, Speleman F, Legius E, Messiaen L.

Hum Mutat. 2006 Oct;27(10):1030-40.

PubMed [citation]

PMID:: 16941471

See all PubMed Citations (9)

Details of each submission

From GeneDx, SCV000322356.10

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

Description

Nonsense 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; This variant is associated with the following publications: (PMID: 10862084, 29957862, 16941471, 21354044, 18041031, 12552569, 17209131, 24676424, 22155606, 24789688, 27838393, 31717729, 31533797, 34427956, 31980526, 17914445, 10607834, 9180088, 25525159, 14517963, 23668869, 24932921, 29506128, 30530636, 10712197, 16479075, 26969325, 15060124, 15146469, 20687928, 31730495, 31533651, 31370276, 29625052, 32005694, 34426522, 34055682, 31776437, 33344560, 31783133)

#	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 Athena Diagnostics, SCV000842891.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

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

From Laboratoire de Génétique Moléculaire, CHU Bordeaux, SCV002568857.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV004026311.1

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

Description

PVS1, PP5, PP1, BS2

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

From CeGaT Center for Human Genetics Tuebingen, SCV004041991.6

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

Description

NF1: PVS1, PM2, PM6, PS4:Moderate, PP1

#	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		1	not provided	not provided	not provided

Last Updated: May 12, 2024

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