VCV002624633.3 - ClinVar

NM_001370259.2(MEN1):c.1795A>T (p.Thr599Ser)

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_001370259.2(MEN1):c.1795A>T (p.Thr599Ser)

Variation ID: 2624633 Accession: VCV002624633.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11q13.1 11: 64804372 (GRCh38) [ NCBI UCSC ] 11: 64571844 (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	Oct 28, 2023	May 1, 2024	Jan 17, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001370259.2:c.1795A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001357188.2:p.Thr599Ser	missense
NM_000244.4:c.1810A>T	NP_000235.3:p.Thr604Ser	missense
NM_001370251.2:c.1921A>T	NP_001357180.2:p.Thr641Ser	missense
NM_001370260.2:c.1795A>T	NP_001357189.2:p.Thr599Ser	missense
NM_001370261.2:c.1795A>T	NP_001357190.2:p.Thr599Ser	missense
NM_001370262.2:c.1690A>T	NP_001357191.2:p.Thr564Ser	missense
NM_001370263.2:c.1690A>T	NP_001357192.2:p.Thr564Ser	missense
NM_001407142.1:c.1921A>T	NP_001394071.1:p.Thr641Ser	missense
NM_001407143.1:c.1921A>T	NP_001394072.1:p.Thr641Ser	missense
NM_001407144.1:c.1921A>T	NP_001394073.1:p.Thr641Ser	missense
NM_001407145.1:c.1810A>T	NP_001394074.1:p.Thr604Ser	missense
NM_001407146.1:c.1795A>T	NP_001394075.1:p.Thr599Ser	missense
NM_001407147.1:c.1795A>T	NP_001394076.1:p.Thr599Ser	missense
NM_001407148.1:c.1690A>T	NP_001394077.1:p.Thr564Ser	missense
NM_001407149.1:c.1690A>T	NP_001394078.1:p.Thr564Ser	missense
NM_001407150.1:c.1936A>T	NP_001394079.1:p.Thr646Ser	missense
NM_001407151.1:c.1816A>T	NP_001394080.1:p.Thr606Ser	missense
NM_001407152.1:c.1630A>T	NP_001394081.1:p.Thr544Ser	missense
NM_130799.3:c.1795A>T	NP_570711.2:p.Thr599Ser	missense
NM_130800.3:c.1810A>T	NP_570712.2:p.Thr604Ser	missense
NM_130801.3:c.1810A>T	NP_570713.2:p.Thr604Ser	missense
NM_130802.3:c.1810A>T	NP_570714.2:p.Thr604Ser	missense
NM_130803.3:c.1810A>T	NP_570715.2:p.Thr604Ser	missense
NM_130804.3:c.1810A>T	NP_570716.2:p.Thr604Ser	missense
NR_176284.1:n.1993A>T		non-coding transcript variant
NR_176285.1:n.2005A>T		non-coding transcript variant
NR_176286.1:n.2008A>T		non-coding transcript variant
NR_176287.1:n.2266A>T		non-coding transcript variant
NC_000011.10:g.64804372T>A
NC_000011.9:g.64571844T>A
NG_008929.1:g.11923A>T
NG_033040.1:g.3870A>T
NG_033040.2:g.3842A>T
LRG_509:g.11923A>T
LRG_509t1:c.1810A>T	LRG_509p1:p.Thr604Ser
LRG_509t2:c.1795A>T	LRG_509p2:p.Thr599Ser

... more HGVS ... less HGVS

Protein change

T604S, T544S, T564S, T606S, T599S, T646S, T641S

Other names

Canonical SPDI

NC_000011.10:64804371:T: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.
MEN1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2579	2600

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	Aug 3, 2023	RCV003386944.2
Multiple endocrine neoplasia, type 1	Uncertain significance (1)	criteria provided, single submitter	Jan 17, 2024	RCV003631316.2

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 17, 2024)	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: SCV004450620.1 First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024	Comment: This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 599 of the MEN1 protein (p.Thr599Ser). … (more) This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 599 of the MEN1 protein (p.Thr599Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MEN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2624633). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MEN1 protein function. 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 (Aug 03, 2023)	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: SCV004091390.2 First in ClinVar: Oct 28, 2023 Last updated: May 01, 2024	Comment: The p.T599S variant (also known as c.1795A>T), located in coding exon 9 of the MEN1 gene, results from an A to T substitution at nucleotide … (more) The p.T599S variant (also known as c.1795A>T), located in coding exon 9 of the MEN1 gene, results from an A to T substitution at nucleotide position 1795. The threonine at codon 599 is replaced by serine, an amino acid with similar properties. This amino acid position is conserved. 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. (less)

Comment:

This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 599 of the MEN1 protein (p.Thr599Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MEN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2624633). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MEN1 protein function. 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.T599S variant (also known as c.1795A>T), located in coding exon 9 of the MEN1 gene, results from an A to T substitution at nucleotide position 1795. The threonine at codon 599 is replaced by serine, an amino acid with similar properties. This amino acid position is conserved. 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.

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.1795A>T (p.Thr599Ser)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...