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NM_000535.7(PMS2):c.1144+1G>C AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 13, 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:
RCV003303232.2

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

NM_000535.7(PMS2):c.1144+1G>C

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.1144+1G>C
HGVS:
  • NC_000007.14:g.5989799C>G
  • NG_008466.1:g.24308G>C
  • NM_000535.5:c.1144+1G>C
  • NM_000535.7:c.1144+1G>CMANE SELECT
  • NM_001322003.2:c.739+1G>C
  • NM_001322004.2:c.739+1G>C
  • NM_001322005.2:c.739+1G>C
  • NM_001322006.2:c.988+2174G>C
  • NM_001322007.2:c.826+1G>C
  • NM_001322008.2:c.826+1G>C
  • NM_001322009.2:c.739+1G>C
  • NM_001322010.2:c.583+2174G>C
  • NM_001322011.2:c.211+1G>C
  • NM_001322012.2:c.211+1G>C
  • NM_001322013.2:c.571+1G>C
  • NM_001322014.2:c.1144+1G>C
  • NM_001322015.2:c.835+1G>C
  • NM_001406866.1:c.1330+1G>C
  • NM_001406868.1:c.1168+1G>C
  • NM_001406869.1:c.1036+1G>C
  • NM_001406870.1:c.988+2174G>C
  • NM_001406871.1:c.1144+1G>C
  • NM_001406872.1:c.1144+1G>C
  • NM_001406873.1:c.946+1G>C
  • NM_001406874.1:c.976+1G>C
  • NM_001406875.1:c.835+1G>C
  • NM_001406876.1:c.826+1G>C
  • NM_001406877.1:c.835+1G>C
  • NM_001406878.1:c.835+1G>C
  • NM_001406879.1:c.835+1G>C
  • NM_001406880.1:c.835+1G>C
  • NM_001406881.1:c.835+1G>C
  • NM_001406882.1:c.835+1G>C
  • NM_001406883.1:c.826+1G>C
  • NM_001406884.1:c.820+2174G>C
  • NM_001406885.1:c.808+1G>C
  • NM_001406886.1:c.778+1G>C
  • NM_001406887.1:c.739+1G>C
  • NM_001406888.1:c.739+1G>C
  • NM_001406889.1:c.739+1G>C
  • NM_001406890.1:c.739+1G>C
  • NM_001406891.1:c.739+1G>C
  • NM_001406892.1:c.739+1G>C
  • NM_001406893.1:c.739+1G>C
  • NM_001406894.1:c.739+1G>C
  • NM_001406895.1:c.739+1G>C
  • NM_001406896.1:c.739+1G>C
  • NM_001406897.1:c.739+1G>C
  • NM_001406898.1:c.739+1G>C
  • NM_001406899.1:c.739+1G>C
  • NM_001406900.1:c.679+2174G>C
  • NM_001406901.1:c.670+2174G>C
  • NM_001406902.1:c.670+2174G>C
  • NM_001406903.1:c.826+1G>C
  • NM_001406904.1:c.631+1G>C
  • NM_001406905.1:c.631+1G>C
  • NM_001406906.1:c.583+2174G>C
  • NM_001406907.1:c.583+2174G>C
  • NM_001406908.1:c.739+1G>C
  • NM_001406909.1:c.571+1G>C
  • NM_001406910.1:c.739+1G>C
  • NM_001406911.1:c.373+1G>C
  • NM_001406912.1:c.804-6808G>C
  • LRG_161t1:c.1144+1G>C
  • LRG_161:g.24308G>C
  • NC_000007.13:g.6029430C>G
  • NM_000535.6:c.1144+1G>C
Links:
dbSNP: rs373885654
NCBI 1000 Genomes Browser:
rs373885654
Molecular consequence:
  • NM_001322006.2:c.988+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.583+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406870.1:c.988+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406884.1:c.820+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406900.1:c.679+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406901.1:c.670+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406902.1:c.670+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406906.1:c.583+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406907.1:c.583+2174G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406912.1:c.804-6808G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.1144+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322003.2:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322004.2:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322005.2:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322007.2:c.826+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322008.2:c.826+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322009.2:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322011.2:c.211+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322012.2:c.211+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322013.2:c.571+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322014.2:c.1144+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322015.2:c.835+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406866.1:c.1330+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406868.1:c.1168+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406869.1:c.1036+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406871.1:c.1144+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406872.1:c.1144+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406873.1:c.946+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406874.1:c.976+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406875.1:c.835+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406876.1:c.826+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406877.1:c.835+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406878.1:c.835+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406879.1:c.835+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406880.1:c.835+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406881.1:c.835+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406882.1:c.835+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406883.1:c.826+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406885.1:c.808+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406886.1:c.778+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406887.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406888.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406889.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406890.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406891.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406892.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406893.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406894.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406895.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406896.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406897.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406898.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406899.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406903.1:c.826+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406904.1:c.631+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406905.1:c.631+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406908.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406909.1:c.571+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406910.1:c.739+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406911.1:c.373+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

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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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003995811Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Jun 13, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV003995811.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1144+1G>C intronic variant results from a G to C substitution one nucleotide after coding exon 10 of the PMS2 gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown; however, a significant portion of the protein is affected (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

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

Last Updated: Sep 29, 2024