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NM_000535.7(PMS2):c.400C>T (p.Arg134Ter) AND Mismatch repair cancer syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 13, 2019
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:
RCV001196700.3

Allele description [Variation Report for NM_000535.7(PMS2):c.400C>T (p.Arg134Ter)]

NM_000535.7(PMS2):c.400C>T (p.Arg134Ter)

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.400C>T (p.Arg134Ter)
Other names:
p.R134*:CGA>TGA
HGVS:
  • NC_000007.14:g.6002590G>A
  • NG_008466.1:g.11517C>T
  • NM_000535.7:c.400C>TMANE SELECT
  • NM_001322003.2:c.-6C>T
  • NM_001322004.2:c.-6C>T
  • NM_001322005.2:c.-6C>T
  • NM_001322006.2:c.400C>T
  • NM_001322007.2:c.82C>T
  • NM_001322008.2:c.82C>T
  • NM_001322009.2:c.-6C>T
  • NM_001322010.2:c.-6C>T
  • NM_001322011.2:c.-485C>T
  • NM_001322012.2:c.-485C>T
  • NM_001322013.2:c.-6C>T
  • NM_001322014.2:c.400C>T
  • NM_001322015.2:c.91C>T
  • NP_000526.2:p.Arg134Ter
  • NP_001308935.1:p.Arg134Ter
  • NP_001308936.1:p.Arg28Ter
  • NP_001308937.1:p.Arg28Ter
  • NP_001308943.1:p.Arg134Ter
  • NP_001308944.1:p.Arg31Ter
  • LRG_161t1:c.400C>T
  • LRG_161:g.11517C>T
  • NC_000007.13:g.6042221G>A
  • NM_000535.5:c.400C>T
  • NM_000535.6:c.400C>T
  • NR_136154.1:n.487C>T
  • p.Arg134Stop
  • p.Arg134X
  • p.R134*
Protein change:
R134*; ARG134TER
Links:
OMIM: 600259.0001; dbSNP: rs63750871
NCBI 1000 Genomes Browser:
rs63750871
Molecular consequence:
  • NM_001322003.2:c.-6C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322004.2:c.-6C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322005.2:c.-6C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322009.2:c.-6C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322010.2:c.-6C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322011.2:c.-485C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-485C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.-6C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_136154.1:n.487C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.400C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322006.2:c.400C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322007.2:c.82C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322008.2:c.82C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322014.2:c.400C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322015.2:c.91C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Mismatch repair cancer syndrome 1 (MMRCS1)
Synonyms:
BRAIN TUMOR-POLYPOSIS SYNDROME 1; BTP1 SYNDROME; CHILDHOOD CANCER SYNDROME; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010159; MedGen: C5399763; Orphanet: 252202; OMIM: 276300

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001367331Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 13, 2019) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001367331.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PM2.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024