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NM_000535.7(PMS2):c.2404C>T (p.Arg802Ter) AND Mismatch repair cancer syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 6, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000009818.5

Allele description [Variation Report for NM_000535.7(PMS2):c.2404C>T (p.Arg802Ter)]

NM_000535.7(PMS2):c.2404C>T (p.Arg802Ter)

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.2404C>T (p.Arg802Ter)
HGVS:
  • NC_000007.14:g.5977629G>A
  • NG_008466.1:g.36478C>T
  • NM_000535.7:c.2404C>TMANE SELECT
  • NM_001322003.2:c.1999C>T
  • NM_001322004.2:c.1999C>T
  • NM_001322005.2:c.1999C>T
  • NM_001322006.2:c.2248C>T
  • NM_001322007.2:c.2086C>T
  • NM_001322008.2:c.2086C>T
  • NM_001322009.2:c.2032C>T
  • NM_001322010.2:c.1843C>T
  • NM_001322011.2:c.1471C>T
  • NM_001322012.2:c.1471C>T
  • NM_001322013.2:c.1831C>T
  • NM_001322014.2:c.2437C>T
  • NM_001322015.2:c.2095C>T
  • NP_000526.2:p.Arg802Ter
  • NP_001308932.1:p.Arg667Ter
  • NP_001308933.1:p.Arg667Ter
  • NP_001308934.1:p.Arg667Ter
  • NP_001308935.1:p.Arg750Ter
  • NP_001308936.1:p.Arg696Ter
  • NP_001308937.1:p.Arg696Ter
  • NP_001308938.1:p.Arg678Ter
  • NP_001308939.1:p.Arg615Ter
  • NP_001308940.1:p.Arg491Ter
  • NP_001308941.1:p.Arg491Ter
  • NP_001308942.1:p.Arg611Ter
  • NP_001308943.1:p.Arg813Ter
  • NP_001308944.1:p.Arg699Ter
  • LRG_161t1:c.2404C>T
  • LRG_161:g.36478C>T
  • NC_000007.13:g.6017260G>A
  • NM_000535.5:c.2404C>T
  • NM_000535.6:c.2404C>T
  • NR_136154.1:n.2448C>T
  • p.R802*
Protein change:
R491*; ARG802TER
Links:
OMIM: 600259.0004; dbSNP: rs63751466
NCBI 1000 Genomes Browser:
rs63751466
Molecular consequence:
  • NR_136154.1:n.2448C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.2404C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322003.2:c.1999C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322004.2:c.1999C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322005.2:c.1999C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322006.2:c.2248C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322007.2:c.2086C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322008.2:c.2086C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322009.2:c.2032C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322010.2:c.1843C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322011.2:c.1471C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322012.2:c.1471C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322013.2:c.1831C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322014.2:c.2437C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322015.2:c.2095C>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
SCV001431024Institute of Human Genetics, Medical University Innsbruck
no assertion criteria provided
Pathogenic
(May 6, 2020) 		germlineresearch

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedresearch

Citations

PubMed

Constitutional mismatch repair deficiency is the diagnosis in 0.41% of pathogenic NF1/SPRED1 variant negative children suspected of sporadic neurofibromatosis type 1.

Perez-Valencia JA, Gallon R, Chen Y, Koch J, Keller M, Oberhuber K, Gomes A, Zschocke J, Burn J, Jackson MS, Santibanez-Koref M, Messiaen L, Wimmer K.

Genet Med. 2020 Dec;22(12):2081-2088. doi: 10.1038/s41436-020-0925-z. Epub 2020 Aug 10.

PubMed [citation]
PMID:
32773772
PMCID:
PMC7708300

Details of each submission

From Institute of Human Genetics, Medical University Innsbruck, SCV001431024.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)

Description

This variant, NM_000535.6:c.2404C>T, was found in compound heterozygosity with the pathogenic variant NM_000535.6:c.736_741delinsTGTGTGTGAAG. Sample UAB620 in Perez J et al, Genet Med (PMID: 32773772).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2024