VCV001767139.5 - ClinVar

NM_000268.4(NF2):c.1278G>A (p.Met426Ile)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000268.4(NF2):c.1278G>A (p.Met426Ile)

Variation ID: 1767139 Accession: VCV001767139.5

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 22q12.2 22: 29673424 (GRCh38) [ NCBI UCSC ] 22: 30069413 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 29, 2022	May 1, 2024	Jan 27, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000268.4:c.1278G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000259.1:p.Met426Ile	missense
NM_001407053.1:c.1164G>A	NP_001393982.1:p.Met388Ile	missense
NM_001407054.1:c.1155G>A	NP_001393983.1:p.Met385Ile	missense
NM_001407055.1:c.1152G>A	NP_001393984.1:p.Met384Ile	missense
NM_001407056.1:c.1164G>A	NP_001393985.1:p.Met388Ile	missense
NM_001407057.1:c.1143G>A	NP_001393986.1:p.Met381Ile	missense
NM_001407058.1:c.1155G>A	NP_001393987.1:p.Met385Ile	missense
NM_001407059.1:c.1143G>A	NP_001393988.1:p.Met381Ile	missense
NM_001407060.1:c.1278G>A	NP_001393989.1:p.Met426Ile	missense
NM_001407062.1:c.1020G>A	NP_001393991.1:p.Met340Ile	missense
NM_001407063.1:c.1029G>A	NP_001393992.1:p.Met343Ile	missense
NM_001407064.1:c.1029G>A	NP_001393993.1:p.Met343Ile	missense
NM_001407065.1:c.744G>A	NP_001393994.1:p.Met248Ile	missense
NM_001407066.1:c.1278G>A	NP_001393995.1:p.Met426Ile	missense
NM_001407067.1:c.1047G>A	NP_001393996.1:p.Met349Ile	missense
NM_016418.5:c.1278G>A	NP_057502.2:p.Met426Ile	missense
NM_181825.3:c.1278G>A	NP_861546.1:p.Met426Ile	missense
NM_181828.3:c.1152G>A	NP_861966.1:p.Met384Ile	missense
NM_181829.3:c.1155G>A	NP_861967.1:p.Met385Ile	missense
NM_181830.3:c.1029G>A	NP_861968.1:p.Met343Ile	missense
NM_181831.3:c.1029G>A	NP_861969.1:p.Met343Ile	missense
NM_181832.3:c.1278G>A	NP_861970.1:p.Met426Ile	missense
NM_181833.3:c.448-21328G>A		intron variant
NR_156186.2:n.1760G>A		non-coding transcript variant
NC_000022.11:g.29673424G>A
NC_000022.10:g.30069413G>A
NG_009057.1:g.74869G>A
LRG_511:g.74869G>A
LRG_511t1:c.1278G>A	LRG_511p1:p.Met426Ile
LRG_511t2:c.1278G>A	LRG_511p2:p.Met426Ile

... more HGVS ... less HGVS

Protein change

M248I, M340I, M349I, M381I, M343I, M426I, M384I, M385I, M388I

Other names

Canonical SPDI

NC_000022.11:29673423:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
NF2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2086	2134

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Hereditary cancer-predisposing syndrome	Uncertain significance (1)	criteria provided, single submitter	May 28, 2022	RCV002374100.2
Neurofibromatosis, type 2	Uncertain significance (1)	criteria provided, single submitter	Jan 27, 2024	RCV003094819.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Jan 27, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Neurofibromatosis, type 2 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003454328.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Comment: This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 426 of the NF2 protein (p.Met426Ile). … (more) This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 426 of the NF2 protein (p.Met426Ile). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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: 1767139). 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%. 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. (less)
Uncertain significance (May 28, 2022)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Hereditary cancer-predisposing syndrome Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV002688380.2 First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024	Comment: The p.M426I variant (also known as c.1278G>A), located in coding exon 12 of the NF2 gene, results from a G to A substitution at nucleotide … (more) The p.M426I variant (also known as c.1278G>A), located in coding exon 12 of the NF2 gene, results from a G to A substitution at nucleotide position 1278. The methionine at codon 426 is replaced by isoleucine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)

Comment:

This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 426 of the NF2 protein (p.Met426Ile). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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: 1767139). 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%. 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.

Comment:

The p.M426I variant (also known as c.1278G>A), located in coding exon 12 of the NF2 gene, results from a G to A substitution at nucleotide position 1278. The methionine at codon 426 is replaced by isoleucine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_000268.4(NF2):c.1278G>A (p.Met426Ile)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...