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NM_000535.7(PMS2):c.1144+1del AND not provided

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:
RCV001356558.2

Allele description [Variation Report for NM_000535.7(PMS2):c.1144+1del]

NM_000535.7(PMS2):c.1144+1del

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.1144+1del
HGVS:
  • NC_000007.14:g.5989800del
  • NG_008466.1:g.24308del
  • NM_000535.7:c.1144+1delMANE SELECT
  • NM_001322003.2:c.739+1del
  • NM_001322004.2:c.739+1del
  • NM_001322005.2:c.739+1del
  • NM_001322006.2:c.988+2174del
  • NM_001322007.2:c.826+1del
  • NM_001322008.2:c.826+1del
  • NM_001322009.2:c.739+1del
  • NM_001322010.2:c.583+2174del
  • NM_001322011.2:c.211+1del
  • NM_001322012.2:c.211+1del
  • NM_001322013.2:c.571+1del
  • NM_001322014.2:c.1144+1del
  • NM_001322015.2:c.835+1del
  • NM_001406866.1:c.1330+1del
  • NM_001406868.1:c.1168+1del
  • NM_001406869.1:c.1036+1del
  • NM_001406870.1:c.988+2174del
  • NM_001406871.1:c.1144+1del
  • NM_001406872.1:c.1144+1del
  • NM_001406873.1:c.946+1del
  • NM_001406874.1:c.976+1del
  • NM_001406875.1:c.835+1del
  • NM_001406876.1:c.826+1del
  • NM_001406877.1:c.835+1del
  • NM_001406878.1:c.835+1del
  • NM_001406879.1:c.835+1del
  • NM_001406880.1:c.835+1del
  • NM_001406881.1:c.835+1del
  • NM_001406882.1:c.835+1del
  • NM_001406883.1:c.826+1del
  • NM_001406884.1:c.820+2174del
  • NM_001406885.1:c.808+1del
  • NM_001406886.1:c.778+1del
  • NM_001406887.1:c.739+1del
  • NM_001406888.1:c.739+1del
  • NM_001406889.1:c.739+1del
  • NM_001406890.1:c.739+1del
  • NM_001406891.1:c.739+1del
  • NM_001406892.1:c.739+1del
  • NM_001406893.1:c.739+1del
  • NM_001406894.1:c.739+1del
  • NM_001406895.1:c.739+1del
  • NM_001406896.1:c.739+1del
  • NM_001406897.1:c.739+1del
  • NM_001406898.1:c.739+1del
  • NM_001406899.1:c.739+1del
  • NM_001406900.1:c.679+2174del
  • NM_001406901.1:c.670+2174del
  • NM_001406902.1:c.670+2174del
  • NM_001406903.1:c.826+1del
  • NM_001406904.1:c.631+1del
  • NM_001406905.1:c.631+1del
  • NM_001406906.1:c.583+2174del
  • NM_001406907.1:c.583+2174del
  • NM_001406908.1:c.739+1del
  • NM_001406909.1:c.571+1del
  • NM_001406910.1:c.739+1del
  • NM_001406911.1:c.373+1del
  • NM_001406912.1:c.804-6808del
  • LRG_161t1:c.1144+1del
  • LRG_161:g.24308del
  • NC_000007.13:g.6029430del
  • NC_000007.13:g.6029431del
  • NM_000535.5:c.1144+1delG
Links:
dbSNP: rs2128746842
NCBI 1000 Genomes Browser:
rs2128746842
Molecular consequence:
  • NM_001322006.2:c.988+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406870.1:c.988+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406884.1:c.820+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406900.1:c.679+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406901.1:c.670+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406902.1:c.670+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406906.1:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406907.1:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406912.1:c.804-6808del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322003.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322004.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322005.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322007.2:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322008.2:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322009.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322011.2:c.211+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322012.2:c.211+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322013.2:c.571+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322014.2:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322015.2:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406866.1:c.1330+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406868.1:c.1168+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406869.1:c.1036+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406871.1:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406872.1:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406873.1:c.946+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406874.1:c.976+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406875.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406876.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406877.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406878.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406879.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406880.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406881.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406882.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406883.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406885.1:c.808+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406886.1:c.778+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406887.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406888.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406889.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406890.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406891.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406892.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406893.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406894.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406895.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406896.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406897.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406898.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406899.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406903.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406904.1:c.631+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406905.1:c.631+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406908.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406909.1:c.571+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406910.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406911.1:c.373+1del - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001551763Department 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 providedunknownyes1not 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), SCV001551763.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The PMS2 c.1144+1delG was not identified in the literature nor was it identified in the following databases: dbSNP, ClinVar, COGR, Cosmic, MutDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, MMR Gene Unclassified Variants Database, or Insight Hereditary Tumors Database. Furthermore, the variant was not identified in the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project or the Exome Aggregation Consortium (August 8th 2016) control databases. The c.1144+1delG 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 provided1not providednot providednot provided

Last Updated: Sep 29, 2024