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NM_000535.7(PMS2):c.2445+1G>A AND Carcinoma of colon

Germline classification:
Pathogenic (1 submission)
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:
RCV001358239.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2445+1G>A]

NM_000535.7(PMS2):c.2445+1G>A

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.2445+1G>A
HGVS:
  • NC_000007.14:g.5977587C>T
  • NG_008466.1:g.36520G>A
  • NM_000535.7:c.2445+1G>AMANE SELECT
  • NM_001322003.2:c.2040+1G>A
  • NM_001322004.2:c.2040+1G>A
  • NM_001322005.2:c.2040+1G>A
  • NM_001322006.2:c.2289+1G>A
  • NM_001322007.2:c.2127+1G>A
  • NM_001322008.2:c.2127+1G>A
  • NM_001322009.2:c.2073+1G>A
  • NM_001322010.2:c.1884+1G>A
  • NM_001322011.2:c.1512+1G>A
  • NM_001322012.2:c.1512+1G>A
  • NM_001322013.2:c.1872+1G>A
  • NM_001322014.2:c.2478+1G>A
  • NM_001322015.2:c.2136+1G>A
  • NM_001406866.1:c.2631+1G>A
  • NM_001406868.1:c.2469+1G>A
  • NM_001406869.1:c.2337+1G>A
  • NM_001406870.1:c.2322+1G>A
  • NM_001406871.1:c.2301+1G>A
  • NM_001406872.1:c.2277+1G>A
  • NM_001406873.1:c.2247+1G>A
  • NM_001406874.1:c.2277+1G>A
  • NM_001406875.1:c.2169+1G>A
  • NM_001406876.1:c.2160+1G>A
  • NM_001406877.1:c.2136+1G>A
  • NM_001406878.1:c.2136+1G>A
  • NM_001406879.1:c.2136+1G>A
  • NM_001406880.1:c.2136+1G>A
  • NM_001406881.1:c.2136+1G>A
  • NM_001406882.1:c.2136+1G>A
  • NM_001406883.1:c.2127+1G>A
  • NM_001406884.1:c.2121+1G>A
  • NM_001406885.1:c.2109+1G>A
  • NM_001406886.1:c.2079+1G>A
  • NM_001406887.1:c.2073+1G>A
  • NM_001406888.1:c.2073+1G>A
  • NM_001406889.1:c.2040+1G>A
  • NM_001406890.1:c.2040+1G>A
  • NM_001406891.1:c.2040+1G>A
  • NM_001406892.1:c.2040+1G>A
  • NM_001406893.1:c.2040+1G>A
  • NM_001406894.1:c.2040+1G>A
  • NM_001406895.1:c.2040+1G>A
  • NM_001406896.1:c.2040+1G>A
  • NM_001406897.1:c.2040+1G>A
  • NM_001406898.1:c.2040+1G>A
  • NM_001406899.1:c.2040+1G>A
  • NM_001406900.1:c.1980+1G>A
  • NM_001406901.1:c.1971+1G>A
  • NM_001406902.1:c.1971+1G>A
  • NM_001406903.1:c.1959+1G>A
  • NM_001406904.1:c.1932+1G>A
  • NM_001406905.1:c.1932+1G>A
  • NM_001406906.1:c.1884+1G>A
  • NM_001406907.1:c.1884+1G>A
  • NM_001406908.1:c.1872+1G>A
  • NM_001406909.1:c.1872+1G>A
  • NM_001406910.1:c.1728+1G>A
  • NM_001406911.1:c.1674+1G>A
  • NM_001406912.1:c.1242+1G>A
  • LRG_161t1:c.2445+1G>A
  • LRG_161:g.36520G>A
  • NC_000007.13:g.6017218C>T
  • NM_000535.5:c.2445+1G>A
Links:
dbSNP: rs876661113
NCBI 1000 Genomes Browser:
rs876661113
Molecular consequence:
  • NM_000535.7:c.2445+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322003.2:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322004.2:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322005.2:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322006.2:c.2289+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322007.2:c.2127+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322008.2:c.2127+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322009.2:c.2073+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322010.2:c.1884+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322011.2:c.1512+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322012.2:c.1512+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322013.2:c.1872+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322014.2:c.2478+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322015.2:c.2136+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406866.1:c.2631+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406868.1:c.2469+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406869.1:c.2337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406870.1:c.2322+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406871.1:c.2301+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406872.1:c.2277+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406873.1:c.2247+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406874.1:c.2277+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406875.1:c.2169+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406876.1:c.2160+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406877.1:c.2136+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406878.1:c.2136+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406879.1:c.2136+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406880.1:c.2136+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406881.1:c.2136+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406882.1:c.2136+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406883.1:c.2127+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406884.1:c.2121+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406885.1:c.2109+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406886.1:c.2079+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406887.1:c.2073+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406888.1:c.2073+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406889.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406890.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406891.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406892.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406893.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406894.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406895.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406896.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406897.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406898.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406899.1:c.2040+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406900.1:c.1980+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406901.1:c.1971+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406902.1:c.1971+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406903.1:c.1959+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406904.1:c.1932+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406905.1:c.1932+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406906.1:c.1884+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406907.1:c.1884+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406908.1:c.1872+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406909.1:c.1872+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406910.1:c.1728+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406911.1:c.1674+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406912.1:c.1242+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
2

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colon carcinoma
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001553914Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Pathogenicunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes2not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001553914.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

The PMS2 c.2445+1G>A variant was not identified in the literature nor was it identified in the following databases: dbSNP, ClinVar, Cosmic, MutDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors Database. The variant was not identified in the control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The c.2445+1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Sep 29, 2024