NM_000535.7(PMS2):c.2445+1G>A AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 22, 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:: RCV000564513.3

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]

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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type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform 1 [Homo sapie...
type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform 1 [Homo sapiens]
gi|154816186|ref|NP_001094284.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000670837	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Aug 22, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000670837

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Aug 22, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV000670837.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.2445+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 14 of the PMS2 gene. This nucleotide position is completely conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice donor site; however, direct evidence is unavailable. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein. As such, this alteration is classified as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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