NM_001042492.3(NF1):c.7153AACTTT[1] (p.2385NF[1]) AND Neurofibromatosis, type 1

Germline classification:: Pathogenic/Likely pathogenic (6 submissions)
Last evaluated:: Jan 5, 2024
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:: RCV000206539.22

Allele description [Variation Report for NM_001042492.3(NF1):c.7153AACTTT[1] (p.2385NF[1])]

NM_001042492.3(NF1):c.7153AACTTT[1] (p.2385NF[1])

Gene:

NF1:neurofibromin 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

17q11.2

Genomic location:

Preferred name:

NM_001042492.3(NF1):c.7153AACTTT[1] (p.2385NF[1])

HGVS:

NC_000017.11:g.31343099AACTTT[1]
NG_009018.1:g.253123AACTTT[1]
NM_000267.3:c.7090AACTTT[1]
NM_000267.3:c.7096_7101del
NM_001042492.3:c.7153AACTTT[1]MANE SELECT
NP_000258.1:p.2364NF[1]
NP_001035957.1:p.2385NF[1]
LRG_214t1:c.7090AACTTT[1]
LRG_214:g.253123AACTTT[1]
LRG_214p1:p.2364NF[1]
NC_000017.10:g.29670116_29670121del
NC_000017.10:g.29670117AACTTT[1]
NM_000267.3:c.7096_7101del
NM_000267.3:c.7096_7101delAACTTT
NM_001042492.2:c.7159_7164del
NM_001042492.2:c.7159_7164del6
NM_001042492.3:c.7153AACTTT[1]

Links:

dbSNP: rs864622639

NCBI 1000 Genomes Browser:

rs864622639

Molecular consequence:

NM_000267.3:c.7090AACTTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001042492.3:c.7153AACTTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Neurofibromatosis, type 1 (NF1)
Synonyms:: NEUROFIBROMATOSIS, TYPE I; Recklinghausen's disease; Von Recklinghausen disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018975; MedGen: C0027831; Orphanet: 636; OMIM: 162200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000261489	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 5, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 8081387, 10862084, 18546366, 24789688, 28492532
SCV000782100	Center for Human Genetics, Inc, Center for Human Genetics, Inc	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 1, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001218929	Medical Genetics, University of Parma	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 20, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001479216	Genome Diagnostics Laboratory, The Hospital for Sick Children	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 26, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002560558	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003837582	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 9, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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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
not provided	germline	no	not provided	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

Two NF1 mutations: frameshift in the GAP-related domain, and loss of two codons toward the 3' end of the gene.

Abernathy CR, Colman SD, Kousseff BG, Wallace MR.

Hum Mutat. 1994;3(4):347-52.

PubMed [citation]

PMID:: 8081387

Exhaustive mutation analysis of the NF1 gene allows identification of 95% of mutations and reveals a high frequency of unusual splicing defects.

Messiaen LM, Callens T, Mortier G, Beysen D, Vandenbroucke I, Van Roy N, Speleman F, Paepe AD.

Hum Mutat. 2000;15(6):541-55.

PubMed [citation]

PMID:: 10862084

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000261489.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant, c.7096_7101del, results in the deletion of 2 amino acid(s) of the NF1 protein (p.Asn2366_Phe2367del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with neurofibromatosis (PMID: 8081387, 10862084, 18546366, 24789688). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 220715). For these reasons, this variant has been classified as Pathogenic.

#	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 Center for Human Genetics, Inc, Center for Human Genetics, Inc, SCV000782100.1

#	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 Medical Genetics, University of Parma, SCV001218929.1

#	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 Genome Diagnostics Laboratory, The Hospital for Sick Children, SCV001479216.1

#	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 Genome-Nilou Lab, SCV002560558.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV003837582.1

#	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

Last Updated: Oct 26, 2024

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