NM_000268.4(NF2):c.478C>T (p.Arg160Trp) AND Neurofibromatosis, type 2

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 25, 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:: RCV000471284.7

Allele description [Variation Report for NM_000268.4(NF2):c.478C>T (p.Arg160Trp)]

NM_000268.4(NF2):c.478C>T (p.Arg160Trp)

Gene:

NF2:NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.2

Genomic location:

Preferred name:

NM_000268.4(NF2):c.478C>T (p.Arg160Trp)

HGVS:

NC_000022.11:g.29654687C>T
NG_009057.1:g.56132C>T
NM_000268.4:c.478C>TMANE SELECT
NM_016418.5:c.478C>T
NM_181825.3:c.478C>T
NM_181828.3:c.352C>T
NM_181829.3:c.355C>T
NM_181830.3:c.229C>T
NM_181831.3:c.229C>T
NM_181832.3:c.478C>T
NM_181833.3:c.447+12402C>T
NP_000259.1:p.Arg160Trp
NP_000259.1:p.Arg160Trp
NP_057502.2:p.Arg160Trp
NP_861546.1:p.Arg160Trp
NP_861966.1:p.Arg118Trp
NP_861967.1:p.Arg119Trp
NP_861968.1:p.Arg77Trp
NP_861969.1:p.Arg77Trp
NP_861970.1:p.Arg160Trp
LRG_511t1:c.478C>T
LRG_511t2:c.478C>T
LRG_511:g.56132C>T
LRG_511p1:p.Arg160Trp
LRG_511p2:p.Arg160Trp
NC_000022.10:g.30050676C>T
NM_000268.3:c.478C>T
NR_156186.2:n.960C>T

Protein change:

R118W

Links:

dbSNP: rs150667239

NCBI 1000 Genomes Browser:

rs150667239

Molecular consequence:

NM_181833.3:c.447+12402C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000268.4:c.478C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_016418.5:c.478C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181825.3:c.478C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181828.3:c.352C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181829.3:c.355C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181830.3:c.229C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181831.3:c.229C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181832.3:c.478C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_156186.2:n.960C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Neurofibromatosis, type 2 (SWNV)
Synonyms:: NF 2; Neurofibromatosis central type; Acoustic schwannomas bilateral; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007039; MedGen: C0027832; Orphanet: 637; OMIM: 101000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000553671	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 25, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004831790	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (May 16, 2023)	germline	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

SCV000553671

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 25, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004831790

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(May 16, 2023)

germline

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	germline	unknown	2	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Invitae, SCV000553671.7

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

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 160 of the NF2 protein (p.Arg160Trp). This variant is present in population databases (rs150667239, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with NF2-related conditions. ClinVar contains an entry for this variant (Variation ID: 412204). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt NF2 protein function with a negative predictive value of 80%. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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 All of Us Research Program, National Institutes of Health, SCV004831790.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (1)

Description

This missense variant replaces arginine with tryptophan at codon 160 of the NF2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with NF2-related disorders in the literature. This variant has been identified in 3/282752 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		2	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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