NM_001370259.2(MEN1):c.1387G>C (p.Glu463Gln) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Dec 14, 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:: RCV001011215.3

Allele description [Variation Report for NM_001370259.2(MEN1):c.1387G>C (p.Glu463Gln)]

NM_001370259.2(MEN1):c.1387G>C (p.Glu463Gln)

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.1387G>C (p.Glu463Gln)

HGVS:

NC_000011.10:g.64804780C>G
NG_008929.1:g.11515G>C
NG_033040.1:g.3462G>C
NM_000244.4:c.1402G>C
NM_001370251.2:c.1513G>C
NM_001370259.2:c.1387G>CMANE SELECT
NM_001370260.2:c.1387G>C
NM_001370261.2:c.1387G>C
NM_001370262.2:c.1282G>C
NM_001370263.2:c.1282G>C
NM_130799.3:c.1387G>C
NM_130800.3:c.1402G>C
NM_130801.3:c.1402G>C
NM_130802.3:c.1402G>C
NM_130803.3:c.1402G>C
NM_130804.3:c.1402G>C
NP_000235.3:p.Glu468Gln
NP_001357180.2:p.Glu505Gln
NP_001357188.2:p.Glu463Gln
NP_001357189.2:p.Glu463Gln
NP_001357190.2:p.Glu463Gln
NP_001357191.2:p.Glu428Gln
NP_001357192.2:p.Glu428Gln
NP_570711.1:p.Glu463Gln
NP_570711.2:p.Glu463Gln
NP_570712.2:p.Glu468Gln
NP_570713.2:p.Glu468Gln
NP_570714.2:p.Glu468Gln
NP_570715.2:p.Glu468Gln
NP_570716.2:p.Glu468Gln
LRG_509t2:c.1387G>C
LRG_509:g.11515G>C
LRG_509p2:p.Glu463Gln
NC_000011.9:g.64572252C>G
NM_130799.2:c.1387G>C

Protein change:

E428Q

Links:

dbSNP: rs748102589

NCBI 1000 Genomes Browser:

rs748102589

Molecular consequence:

NM_000244.4:c.1402G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370251.2:c.1513G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370259.2:c.1387G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370260.2:c.1387G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370261.2:c.1387G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370262.2:c.1282G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370263.2:c.1282G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_130799.3:c.1387G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_130800.3:c.1402G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_130801.3:c.1402G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_130802.3:c.1402G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_130803.3:c.1402G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_130804.3:c.1402G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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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
SCV001171512	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Dec 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001171512

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Dec 14, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV001171512.4

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Sep 29, 2024

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