NM_000268.4(NF2):c.1439C>A (p.Thr480Lys) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 3, 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:: RCV001011577.3

Allele description [Variation Report for NM_000268.4(NF2):c.1439C>A (p.Thr480Lys)]

NM_000268.4(NF2):c.1439C>A (p.Thr480Lys)

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.1439C>A (p.Thr480Lys)

HGVS:

NC_000022.11:g.29674934C>A
NG_009057.1:g.76379C>A
NM_000268.4:c.1439C>AMANE SELECT
NM_016418.5:c.1439C>A
NM_181825.3:c.1439C>A
NM_181828.3:c.1313C>A
NM_181829.3:c.1316C>A
NM_181830.3:c.1190C>A
NM_181831.3:c.1190C>A
NM_181832.3:c.1439C>A
NM_181833.3:c.448-19818C>A
NP_000259.1:p.Thr480Lys
NP_057502.2:p.Thr480Lys
NP_861546.1:p.Thr480Lys
NP_861966.1:p.Thr438Lys
NP_861967.1:p.Thr439Lys
NP_861968.1:p.Thr397Lys
NP_861969.1:p.Thr397Lys
NP_861970.1:p.Thr480Lys
LRG_511t1:c.1439C>A
LRG_511t2:c.1439C>A
LRG_511:g.76379C>A
LRG_511p2:p.Thr480Lys
NC_000022.10:g.30070923C>A
NC_000022.10:g.30070923C>A
NM_000268.3:c.1439C>A
NR_156186.2:n.1921C>A

Protein change:

T397K

Links:

dbSNP: rs145666157

NCBI 1000 Genomes Browser:

rs145666157

Molecular consequence:

NM_181833.3:c.448-19818C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000268.4:c.1439C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_016418.5:c.1439C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181825.3:c.1439C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181828.3:c.1313C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181829.3:c.1316C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181830.3:c.1190C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181831.3:c.1190C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181832.3:c.1439C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_156186.2:n.1921C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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Homo sapiens calpain 2 (CAPN2), transcript variant 1, mRNA
Homo sapiens calpain 2 (CAPN2), transcript variant 1, mRNA
gi|1519245949|ref|NM_001748.5|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001171914	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 3, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001171914

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 3, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV001171914.4

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

Description

The p.T480K variant (also known as c.1439C>A), located in coding exon 13 of the NF2 gene, results from a C to A substitution at nucleotide position 1439. The threonine at codon 480 is replaced by lysine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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