VCV002808810.2 - ClinVar

NM_001370259.2(MEN1):c.1673T>C (p.Met558Thr)

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.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001370259.2(MEN1):c.1673T>C (p.Met558Thr)

Variation ID: 2808810 Accession: VCV002808810.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11q13.1 11: 64804494 (GRCh38) [ NCBI UCSC ] 11: 64571966 (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	Feb 20, 2024	Aug 11, 2024	May 4, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001370259.2:c.1673T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001357188.2:p.Met558Thr	missense
NM_000244.4:c.1688T>C	NP_000235.3:p.Met563Thr	missense
NM_001370251.2:c.1799T>C	NP_001357180.2:p.Met600Thr	missense
NM_001370260.2:c.1673T>C	NP_001357189.2:p.Met558Thr	missense
NM_001370261.2:c.1673T>C	NP_001357190.2:p.Met558Thr	missense
NM_001370262.2:c.1568T>C	NP_001357191.2:p.Met523Thr	missense
NM_001370263.2:c.1568T>C	NP_001357192.2:p.Met523Thr	missense
NM_001407142.1:c.1799T>C	NP_001394071.1:p.Met600Thr	missense
NM_001407143.1:c.1799T>C	NP_001394072.1:p.Met600Thr	missense
NM_001407144.1:c.1799T>C	NP_001394073.1:p.Met600Thr	missense
NM_001407145.1:c.1688T>C	NP_001394074.1:p.Met563Thr	missense
NM_001407146.1:c.1673T>C	NP_001394075.1:p.Met558Thr	missense
NM_001407147.1:c.1673T>C	NP_001394076.1:p.Met558Thr	missense
NM_001407148.1:c.1568T>C	NP_001394077.1:p.Met523Thr	missense
NM_001407149.1:c.1568T>C	NP_001394078.1:p.Met523Thr	missense
NM_001407150.1:c.1814T>C	NP_001394079.1:p.Met605Thr	missense
NM_001407151.1:c.1694T>C	NP_001394080.1:p.Met565Thr	missense
NM_001407152.1:c.1508T>C	NP_001394081.1:p.Met503Thr	missense
NM_130799.3:c.1673T>C	NP_570711.2:p.Met558Thr	missense
NM_130800.3:c.1688T>C	NP_570712.2:p.Met563Thr	missense
NM_130801.3:c.1688T>C	NP_570713.2:p.Met563Thr	missense
NM_130802.3:c.1688T>C	NP_570714.2:p.Met563Thr	missense
NM_130803.3:c.1688T>C	NP_570715.2:p.Met563Thr	missense
NM_130804.3:c.1688T>C	NP_570716.2:p.Met563Thr	missense
NR_176284.1:n.1871T>C		non-coding transcript variant
NR_176285.1:n.1883T>C		non-coding transcript variant
NR_176286.1:n.1886T>C		non-coding transcript variant
NR_176287.1:n.2144T>C		non-coding transcript variant
NC_000011.10:g.64804494A>G
NC_000011.9:g.64571966A>G
NG_008929.1:g.11801T>C
NG_033040.1:g.3748T>C
NG_033040.2:g.3720T>C
LRG_509:g.11801T>C
LRG_509t1:c.1688T>C	LRG_509p1:p.Met563Thr
LRG_509t2:c.1673T>C	LRG_509p2:p.Met558Thr

... more HGVS ... less HGVS

Protein change

M523T, M563T, M605T, M503T, M558T, M565T, M600T

Other names

Canonical SPDI

NC_000011.10:64804493:A:G

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.
MEN1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2580	2601

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.
Multiple endocrine neoplasia, type 1	Likely pathogenic (1)	criteria provided, single submitter	Oct 5, 2023	RCV003631631.2
Hereditary cancer-predisposing syndrome	Uncertain significance (1)	criteria provided, single submitter	May 4, 2024	RCV004636796.1

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.
Likely pathogenic (Oct 05, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Multiple endocrine neoplasia, type 1 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004405623.1 First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024	Comment: This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 558 of the MEN1 protein (p.Met558Thr). … (more) This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 558 of the MEN1 protein (p.Met558Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of multiple endocrine neoplasia type 1 (Invitae). 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 expected to disrupt MEN1 protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. (less)
Uncertain significance (May 04, 2024)	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: SCV005131152.1 First in ClinVar: Aug 11, 2024 Last updated: Aug 11, 2024	Comment: The p.M558T variant (also known as c.1673T>C), located in coding exon 9 of the MEN1 gene, results from a T to C substitution at nucleotide … (more) The p.M558T variant (also known as c.1673T>C), located in coding exon 9 of the MEN1 gene, results from a T to C substitution at nucleotide position 1673. The methionine at codon 558 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. (less)

Comment:

This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 558 of the MEN1 protein (p.Met558Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of multiple endocrine neoplasia type 1 (Invitae). 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 expected to disrupt MEN1 protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

Comment:

The p.M558T variant (also known as c.1673T>C), located in coding exon 9 of the MEN1 gene, results from a T to C substitution at nucleotide position 1673. The methionine at codon 558 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant 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 30, 2024

ClinVar Genomic variation as it relates to human health

NM_001370259.2(MEN1):c.1673T>C (p.Met558Thr)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...