NM_001370259.2(MEN1):c.1379G>A (p.Arg460Gln) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Nov 16, 2023
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:: RCV000034783.2

Allele description [Variation Report for NM_001370259.2(MEN1):c.1379G>A (p.Arg460Gln)]

NM_001370259.2(MEN1):c.1379G>A (p.Arg460Gln)

Gene:

MEN1:menin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_001370259.2(MEN1):c.1379G>A (p.Arg460Gln)

HGVS:

NC_000011.10:g.64804788C>T
NG_008929.1:g.11507G>A
NG_033040.1:g.3454G>A
NM_000244.4:c.1394G>A
NM_001370251.2:c.1505G>A
NM_001370259.2:c.1379G>AMANE SELECT
NM_001370260.2:c.1379G>A
NM_001370261.2:c.1379G>A
NM_001370262.2:c.1274G>A
NM_001370263.2:c.1274G>A
NM_130799.3:c.1379G>A
NM_130800.3:c.1394G>A
NM_130801.3:c.1394G>A
NM_130802.3:c.1394G>A
NM_130803.3:c.1394G>A
NM_130804.3:c.1394G>A
NP_000235.3:p.Arg465Gln
NP_001357180.2:p.Arg502Gln
NP_001357188.2:p.Arg460Gln
NP_001357189.2:p.Arg460Gln
NP_001357190.2:p.Arg460Gln
NP_001357191.2:p.Arg425Gln
NP_001357192.2:p.Arg425Gln
NP_570711.1:p.Arg460Gln
NP_570711.2:p.Arg460Gln
NP_570712.2:p.Arg465Gln
NP_570713.2:p.Arg465Gln
NP_570714.2:p.Arg465Gln
NP_570715.2:p.Arg465Gln
NP_570716.2:p.Arg465Gln
LRG_509t2:c.1379G>A
LRG_509:g.11507G>A
LRG_509p2:p.Arg460Gln
NC_000011.9:g.64572260C>T
NM_130799.2:c.1379G>A

Protein change:

R425Q

Links:

dbSNP: rs200035619

NCBI 1000 Genomes Browser:

rs200035619

Molecular consequence:

NM_000244.4:c.1394G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370251.2:c.1505G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370259.2:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370260.2:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370261.2:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370262.2:c.1274G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370263.2:c.1274G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130799.3:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130800.3:c.1394G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130801.3:c.1394G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130802.3:c.1394G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130803.3:c.1394G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130804.3:c.1394G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Trmt10c tRNA methyltransferase 10C, mitochondrial RNase P subunit [Mus musculus]
Trmt10c tRNA methyltransferase 10C, mitochondrial RNase P subunit [Mus musculus]
Gene ID:52575

Gene
52575[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000043286	Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq	no assertion criteria provided	variant of unknown significance (Jul 13, 2012)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV005199116	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 16, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000043286

Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq

no assertion criteria provided

variant of unknown significance
(Jul 13, 2012)

germline

research

PubMed (1)
[See all records that cite this PMID]

SCV005199116

Clinical Genetics Laboratory, Skane University Hospital Lund

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 16, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	1	not provided	not provided	487	not provided	research
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes.

Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG.

Am J Hum Genet. 2012 Jul 13;91(1):97-108. doi: 10.1016/j.ajhg.2012.05.021. Epub 2012 Jun 14.

PubMed [citation]

PMID:: 22703879
PMCID:: PMC3397257

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq, SCV000043286.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	PubMed (1)

Description

The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See PubMed ID:22703879 for details.

Description

Converted during submission to Uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	487	not provided	discovery		1	not provided	not provided	not provided

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005199116.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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