NM_000268.4(NF2):c.300T>A (p.Phe100Leu) AND Neurofibromatosis, type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 28, 2022
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:: RCV000526156.9

Allele description [Variation Report for NM_000268.4(NF2):c.300T>A (p.Phe100Leu)]

NM_000268.4(NF2):c.300T>A (p.Phe100Leu)

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.300T>A (p.Phe100Leu)

HGVS:

NC_000022.11:g.29639149T>A
NG_009057.1:g.40594T>A
NM_000268.4:c.300T>AMANE SELECT
NM_016418.5:c.300T>A
NM_181825.3:c.300T>A
NM_181828.3:c.174T>A
NM_181829.3:c.240+2273T>A
NM_181830.3:c.115-3053T>A
NM_181831.3:c.115-3053T>A
NM_181832.3:c.300T>A
NM_181833.3:c.300T>A
NP_000259.1:p.Phe100Leu
NP_000259.1:p.Phe100Leu
NP_057502.2:p.Phe100Leu
NP_861546.1:p.Phe100Leu
NP_861966.1:p.Phe58Leu
NP_861970.1:p.Phe100Leu
NP_861971.1:p.Phe100Leu
LRG_511t1:c.300T>A
LRG_511t2:c.300T>A
LRG_511:g.40594T>A
LRG_511p1:p.Phe100Leu
LRG_511p2:p.Phe100Leu
NC_000022.10:g.30035138T>A
NM_000268.3:c.300T>A
NR_156186.2:n.782T>A

Protein change:

F100L

Links:

dbSNP: rs1555987677

NCBI 1000 Genomes Browser:

rs1555987677

Molecular consequence:

NM_181829.3:c.240+2273T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_181830.3:c.115-3053T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_181831.3:c.115-3053T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000268.4:c.300T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_016418.5:c.300T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181825.3:c.300T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181828.3:c.174T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181832.3:c.300T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181833.3:c.300T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_156186.2:n.782T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Recent activity

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dysferlin isoform X1 [Acanthopagrus latus]
dysferlin isoform X1 [Acanthopagrus latus]
gi|1927197670|ref|XP_036967643.1|

Protein
LAMA2 [Mustela nigripes]
LAMA2 [Mustela nigripes]
Gene ID:132018153

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000628867	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 28, 2022)	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

SCV000628867

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 28, 2022)

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	not provided	not provided	not provided	not provided	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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000628867.6

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). ClinVar contains an entry for this variant (Variation ID: 457913). This variant has not been reported in the literature in individuals affected with NF2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 100 of the NF2 protein (p.Phe100Leu).

#	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

Last Updated: Sep 29, 2024

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