ClinVar Genomic variation as it relates to human health
NM_001370259.2(MEN1):c.1378C>T (p.Arg460Ter)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001370259.2(MEN1):c.1378C>T (p.Arg460Ter)
Variation ID: 16692 Accession: VCV000016692.29
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11q13.1 11: 64804789 (GRCh38) [ NCBI UCSC ] 11: 64572261 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Apr 4, 2013 May 1, 2024 Jan 30, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370259.2:c.1378C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357188.2:p.Arg460Ter nonsense NM_000244.4:c.1393C>T NP_000235.3:p.Arg465Ter nonsense NM_001370251.2:c.1504C>T NP_001357180.2:p.Arg502Ter nonsense NM_001370260.2:c.1378C>T NP_001357189.2:p.Arg460Ter nonsense NM_001370261.2:c.1378C>T NP_001357190.2:p.Arg460Ter nonsense NM_001370262.2:c.1273C>T NP_001357191.2:p.Arg425Ter nonsense NM_001370263.2:c.1273C>T NP_001357192.2:p.Arg425Ter nonsense NM_130799.3:c.1378C>T NP_570711.2:p.Arg460Ter nonsense NM_130800.3:c.1393C>T NP_570712.2:p.Arg465Ter nonsense NM_130801.3:c.1393C>T NP_570713.2:p.Arg465Ter nonsense NM_130802.3:c.1393C>T NP_570714.2:p.Arg465Ter nonsense NM_130803.3:c.1393C>T NP_570715.2:p.Arg465Ter nonsense NM_130804.3:c.1393C>T NP_570716.2:p.Arg465Ter nonsense NC_000011.10:g.64804789G>A NC_000011.9:g.64572261G>A NG_008929.1:g.11506C>T NG_033040.1:g.3453C>T LRG_509:g.11506C>T LRG_509t1:c.1393C>T LRG_509p1:p.Arg465Ter LRG_509t2:c.1378C>T LRG_509p2:p.Arg460Ter - Protein change
- R460*, R465*, R502*, R425*
- Other names
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p.R460*:CGA>TGA
- Canonical SPDI
- NC_000011.10:64804788:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe 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.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00000
The Genome Aggregation Database (gnomAD) 0.00001
- Links
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 | ||
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HI score
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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. |
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MEN1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
2581 | 2602 |
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. |
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Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Jan 30, 2024 | RCV000018172.15 | |
Pathogenic (1) |
criteria provided, single submitter
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May 24, 2017 | RCV000129526.3 | |
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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Aug 1, 2019 | RCV000182421.20 |
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. |
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Pathogenic
(Mar 02, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000700503.2
First in ClinVar: Oct 11, 2015 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Pathogenic
(Aug 25, 2017)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000885689.1
First in ClinVar: Dec 15, 2018 Last updated: Dec 15, 2018 |
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Pathogenic
(Feb 27, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics and Genomics, Karolinska University Hospital
Accession: SCV001449957.1
First in ClinVar: Dec 11, 2020 Last updated: Dec 11, 2020 |
Number of individuals with the variant: 1
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Pathogenic
(Aug 01, 2019)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000234766.10
First in ClinVar: Jul 05, 2015 Last updated: Apr 17, 2019 |
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more)
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 9554741, 18753103, 29922966, 30339208, 10715991, 9215689, 11836268, 27212590, 22026581, 26767918, 26905068, 14678300, 27588171, 21819486, 28785839, 30342802) (less)
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Pathogenic
(Jan 30, 2024)
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criteria provided, single submitter
Method: clinical testing
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Multiple endocrine neoplasia, type 1
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000953567.6
First in ClinVar: Aug 14, 2019 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg460*) in the MEN1 gene. While this is not anticipated to result in nonsense mediated decay, … (more)
This sequence change creates a premature translational stop signal (p.Arg460*) in the MEN1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 151 amino acid(s) of the MEN1 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with multiple endocrine neoplasia type 1 (PMID: 9215689, 14678300, 17879353, 18753103, 19461164). ClinVar contains an entry for this variant (Variation ID: 16692). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects MEN1 function (PMID: 21819486). This variant disrupts a region of the MEN1 protein in which other variant(s) (p.Arg516Glyfs*43) have been determined to be pathogenic (PMID: 17879353). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(May 24, 2017)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000184302.4
First in ClinVar: Aug 06, 2014 Last updated: May 01, 2024 |
Comment:
The p.R460* pathogenic mutation (also known as c.1378C>T), located in coding exon 9 of the MEN1 gene, results from a C to T substitution at … (more)
The p.R460* pathogenic mutation (also known as c.1378C>T), located in coding exon 9 of the MEN1 gene, results from a C to T substitution at nucleotide position 1378. This changes the amino acid from an arginine to a stop codon within coding exon 9. This alteration has been identified in many unrelated patients and families with MEN1 (Agarwal SK et al. Hum Mol Genet.1997;6(7):1169-75; Matsuzaki LN et al. Clin Endocrinol (Oxf). 2004;60(1):142-3; Goroshi M et al. Fam. Cancer. 2016 Oct;15(4):617-24). In addition, this mutation has demonstrated expression levels at less than 20% compared to wild type in an in vitro study (Shimazu S et al. Cancer Sci. 2011 Nov;102(11):2097-102). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation. As such, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(Jul 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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Multiple endocrine neoplasia, type 1
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004189096.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
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Pathogenic
(Oct 04, 2012)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV002774386.2
First in ClinVar: Dec 31, 2022 Last updated: Jan 06, 2024 |
Comment:
This nonsense variant causes the premature termination of MEN1 protein synthesis. In addition, it has been reported in individuals affected with Multiple Endocrine Neoplasia Type … (more)
This nonsense variant causes the premature termination of MEN1 protein synthesis. In addition, it has been reported in individuals affected with Multiple Endocrine Neoplasia Type 1 (MEN1) syndrome in the published literature (PMID: 17879353 (2008), 12049533 (2002), 9683585 (1998), 9215689 (1997)). Based on the available information, this variant is classified as pathogenic. (less)
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Pathogenic
(Jan 01, 1998)
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no assertion criteria provided
Method: literature only
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MULTIPLE ENDOCRINE NEOPLASIA, TYPE I
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000038451.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
Olufemi et al. (1998) demonstrated an arg460-to-ter mutation (R460X) in the MEN1 gene in affected members of 4 families with MEN1 (131100), originally described by … (more)
Olufemi et al. (1998) demonstrated an arg460-to-ter mutation (R460X) in the MEN1 gene in affected members of 4 families with MEN1 (131100), originally described by Farid et al. (1980) and Bear et al. (1985). Affected members had prolactinomas, carcinoid tumors of the lung and thymus, and hyperparathyroidism. The disorder was called the MEN1 Burin variant by Bear et al. (1985). All 4 families lived in the Burin peninsula of Newfoundland. The ancestors of each of the 4 independently identified families came from a group of very small, isolated, now-abandoned communities within a 20-mile radius on the north shore of Fortune Bay. No single common ancestor was identified by examination of genealogic records, but there were common surnames in the earliest generations recorded. By haplotype analysis, Olufemi et al. (1998) demonstrated a common haplotype over a 2.5-Mb region that was shared by affected members of all 4 families. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Multiple endocrine neoplasia, type 1
Affected status: unknown
Allele origin:
germline
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GeneReviews
Accession: SCV002549164.2
First in ClinVar: Jul 22, 2022 Last updated: Oct 01, 2022 |
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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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Multiple Endocrine Neoplasia Type 1. | Adam MP | - | 2022 | PMID: 20301710 |
Multiple endocrine neoplasia type 1 syndrome: single centre experience from western India. | Goroshi M | Familial cancer | 2016 | PMID: 26905068 |
Correlation of mutant menin stability with clinical expression of multiple endocrine neoplasia type 1 and its incomplete forms. | Shimazu S | Cancer science | 2011 | PMID: 21819486 |
Multiple endocrine neoplasia type 1 (MEN1). | Thakker RV | Best practice & research. Clinical endocrinology & metabolism | 2010 | PMID: 20833329 |
MEN1 gene analysis in patients with primary hyperparathyroidism: 10-year experience of a single institution for thyroid and parathyroid care in Japan. | Kihara M | Endocrine journal | 2009 | PMID: 19461164 |
Gonadotroph adenoma in multiple endocrine neoplasia type 1. | Sztal-Mazer S | Endocrine practice : official journal of the American College of Endocrinology and the American Association of Clinical Endocrinologists | 2008 | PMID: 18753103 |
Effect of treatment with depot somatostatin analogue octreotide on primary hyperparathyroidism (PHP) in multiple endocrine neoplasia type 1 (MEN1) patients. | Faggiano A | Clinical endocrinology | 2008 | PMID: 18485119 |
Multiple endocrine neoplasia type 1 (MEN1): analysis of 1336 mutations reported in the first decade following identification of the gene. | Lemos MC | Human mutation | 2008 | PMID: 17879353 |
Rapid mutation screening for HRPT2 and MEN1 mutations associated with familial and sporadic primary hyperparathyroidism. | Howell VM | The Journal of molecular diagnostics : JMD | 2006 | PMID: 17065424 |
Characteristics of the Danish families with multiple endocrine neoplasia type 1. | Jäger AC | Molecular and cellular endocrinology | 2006 | PMID: 16563611 |
Tumor suppressor menin: the essential role of nuclear localization signal domains in coordinating gene expression. | La P | Oncogene | 2006 | PMID: 16449969 |
Clinical testing for multiple endocrine neoplasia type 1 in a DNA diagnostic laboratory. | Klein RD | Genetics in medicine : official journal of the American College of Medical Genetics | 2005 | PMID: 15714081 |
Detection of an MEN1 gene mutation depends on clinical features and supports current referral criteria for diagnostic molecular genetic testing. | Ellard S | Clinical endocrinology | 2005 | PMID: 15670192 |
A report of a national mutation testing service for the MEN1 gene: clinical presentations and implications for mutation testing. | Cardinal JW | Journal of medical genetics | 2005 | PMID: 15635078 |
Direct binding of DNA by tumor suppressor menin. | La P | The Journal of biological chemistry | 2004 | PMID: 15331604 |
Multiple endocrine neoplasia type 1 variant with frequent prolactinoma and rare gastrinoma. | Hao W | The Journal of clinical endocrinology and metabolism | 2004 | PMID: 15292304 |
Cushing's disease as the first clinical manifestation of multiple endocrine neoplasia type 1 (MEN1) associated with an R460X mutation of the MEN1 gene. | Matsuzaki LN | Clinical endocrinology | 2004 | PMID: 14678300 |
Efficient mutation detection in MEN1 gene using a combination of single-strand conformation polymorphism (MDGA) and heteroduplex analysis. | Crépin M | Electrophoresis | 2003 | PMID: 12652570 |
Genotype-phenotype analysis in multiple endocrine neoplasia type 1. | Kouvaraki MA | Archives of surgery (Chicago, Ill. : 1960) | 2002 | PMID: 12049533 |
Pituitary disease in MEN type 1 (MEN1): data from the France-Belgium MEN1 multicenter study. | Vergès B | The Journal of clinical endocrinology and metabolism | 2002 | PMID: 11836268 |
Multiple endocrine neoplasia type 1Burin from Mauritius: a novel MEN1 mutation. | Kong C | Journal of endocrinological investigation | 2001 | PMID: 11765051 |
Molecular and genetic mechanisms of tumorigenesis in multiple endocrine neoplasia type-1. | Guo SS | Molecular endocrinology (Baltimore, Md.) | 2001 | PMID: 11579199 |
Multiple endocrine neoplasia type 1. | Thakker RV | Endocrinology and metabolism clinics of North America | 2000 | PMID: 11033760 |
Multiple endocrine neoplasia type 1: from bedside to benchside. | Yoshimoto K | The journal of medical investigation : JMI | 2000 | PMID: 11019489 |
Identification of MEN1 gene mutations in families with MEN 1 and related disorders. | Bergman L | British journal of cancer | 2000 | PMID: 10993647 |
Somatic mutations of the multiple endocrine neoplasia type 1 (MEN1) gene in patients with sporadic, nonfamilial primary hyperparathyroidism. | Sato K | Surgery | 2000 | PMID: 10715991 |
Multiple endocrine neoplasia type 1. | Pannett AA | Endocrine-related cancer | 1999 | PMID: 10730900 |
Molecular pathology of multiple endocrine neoplasia type I: two novel germline mutations and updated classification of mutations affecting MEN1 gene. | Martín-Campos JM | Diagnostic molecular pathology : the American journal of surgical pathology, part B | 1999 | PMID: 10617276 |
Multiple endocrine neoplasia type 1: clinical and genetic features of the hereditary endocrine neoplasias. | Marx SJ | Recent progress in hormone research | 1999 | PMID: 10548885 |
Germ-line mutation analysis in patients with multiple endocrine neoplasia type 1 and related disorders. | Giraud S | American journal of human genetics | 1998 | PMID: 9683585 |
Germline and somatic mutation of the gene for multiple endocrine neoplasia type 1 (MEN1). | Marx SJ | Journal of internal medicine | 1998 | PMID: 9681842 |
Identification and characterization of the multiple endocrine neoplasia type 1 (MEN1) gene. | Guru SC | Journal of internal medicine | 1998 | PMID: 9681840 |
Analysis of recurrent germline mutations in the MEN1 gene encountered in apparently unrelated families. | Agarwal SK | Human mutation | 1998 | PMID: 9671267 |
Genetic testing in multiple endocrine neoplasia and related syndromes. | Calender A | Forum (Genoa, Italy) | 1998 | PMID: 9666051 |
Common ancestral mutation in the MEN1 gene is likely responsible for the prolactinoma variant of MEN1 (MEN1Burin) in four kindreds from Newfoundland. | Olufemi SE | Human mutation | 1998 | PMID: 9554741 |
Cutaneous tumors in patients with multiple endocrine neoplasia type 1 show allelic deletion of the MEN1 gene. | Pack S | The Journal of investigative dermatology | 1998 | PMID: 9540988 |
Characterization of mutations in patients with multiple endocrine neoplasia type 1. | Bassett JH | American journal of human genetics | 1998 | PMID: 9463336 |
Germline mutations of the MEN1 gene in familial multiple endocrine neoplasia type 1 and related states. | Agarwal SK | Human molecular genetics | 1997 | PMID: 9215689 |
Variant multiple endocrine neoplasia I (MEN IBurin): further studies and non-linkage to HLA. | Bear JC | Human heredity | 1985 | PMID: 2857681 |
Prolactinomas in familial multiple endocrine neoplasia syndrome type I. Relationship to HLA and carcinoid tumors. | Farid NR | The American journal of medicine | 1980 | PMID: 6108714 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MEN1 | - | - | - | - |
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Text-mined citations for rs104894267 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.