NM_000535.7(PMS2):c.162T>C (p.Ile54=) AND Hereditary nonpolyposis colorectal neoplasms
- Germline classification:
- Uncertain significance (1 submission)
- Last evaluated:
- Dec 12, 2023
- Review status:
- 1 star out of maximum of 4 starscriteria provided, single submitter
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV003595171.1
Allele description [Variation Report for NM_000535.7(PMS2):c.162T>C (p.Ile54=)]
NM_000535.7(PMS2):c.162T>C (p.Ile54=)
- 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.162T>C (p.Ile54=)
- HGVS:
- NC_000007.14:g.6005893A>G
- NG_008466.1:g.8214T>C
- NG_050738.1:g.1643A>G
- NM_000535.7:c.162T>CMANE SELECT
- NM_001018040.1:c.-244T>C
- NM_001322003.2:c.-244T>C
- NM_001322004.2:c.-242-1835T>C
- NM_001322005.2:c.-244T>C
- NM_001322006.2:c.162T>C
- NM_001322007.2:c.-54T>C
- NM_001322008.2:c.-52-1835T>C
- NM_001322009.2:c.-244T>C
- NM_001322010.2:c.-242-1835T>C
- NM_001322011.2:c.-723T>C
- NM_001322012.2:c.-723T>C
- NM_001322013.2:c.-244T>C
- NM_001322014.2:c.162T>C
- NM_001322015.2:c.-323T>C
- NM_001406866.1:c.348T>C
- NM_001406868.1:c.162T>C
- NM_001406869.1:c.162T>C
- NM_001406870.1:c.162T>C
- NM_001406871.1:c.162T>C
- NM_001406872.1:c.162T>C
- NM_001406873.1:c.162T>C
- NM_001406874.1:c.162T>C
- NM_001406875.1:c.-323T>C
- NM_001406876.1:c.-54T>C
- NM_001406877.1:c.-323T>C
- NM_001406878.1:c.-323T>C
- NM_001406879.1:c.-321-1835T>C
- NM_001406880.1:c.-270T>C
- NM_001406881.1:c.-218-1835T>C
- NM_001406882.1:c.-323T>C
- NM_001406883.1:c.-54T>C
- NM_001406884.1:c.162T>C
- NM_001406885.1:c.162T>C
- NM_001406886.1:c.162T>C
- NM_001406887.1:c.-244T>C
- NM_001406888.1:c.-191T>C
- NM_001406889.1:c.-191T>C
- NM_001406890.1:c.-234T>C
- NM_001406891.1:c.-244T>C
- NM_001406892.1:c.-191T>C
- NM_001406893.1:c.-244T>C
- NM_001406894.1:c.-191T>C
- NM_001406895.1:c.-189-1835T>C
- NM_001406896.1:c.-54T>C
- NM_001406897.1:c.-244T>C
- NM_001406898.1:c.-244T>C
- NM_001406899.1:c.-191T>C
- NM_001406900.1:c.-220T>C
- NM_001406901.1:c.-54T>C
- NM_001406902.1:c.-54T>C
- NM_001406903.1:c.-54T>C
- NM_001406904.1:c.-191T>C
- NM_001406905.1:c.-244T>C
- NM_001406906.1:c.-244T>C
- NM_001406907.1:c.-191T>C
- NM_001406908.1:c.-244T>C
- NM_001406909.1:c.-191T>C
- NM_001406910.1:c.-244T>C
- NM_001406911.1:c.-242-1835T>C
- NM_001406912.1:c.162T>C
- NP_000526.1:p.Ile54=
- NP_000526.2:p.Ile54=
- NP_001308935.1:p.Ile54=
- NP_001308943.1:p.Ile54=
- NP_001393795.1:p.Ile116=
- NP_001393797.1:p.Ile54=
- NP_001393798.1:p.Ile54=
- NP_001393799.1:p.Ile54=
- NP_001393800.1:p.Ile54=
- NP_001393801.1:p.Ile54=
- NP_001393802.1:p.Ile54=
- NP_001393803.1:p.Ile54=
- NP_001393813.1:p.Ile54=
- NP_001393814.1:p.Ile54=
- NP_001393815.1:p.Ile54=
- NP_001393841.1:p.Ile54=
- LRG_161t1:c.162T>C
- LRG_161:g.8214T>C
- LRG_161p1:p.Ile54=
- NC_000007.13:g.6045524A>G
- NM_000535.5:c.162T>C
- NR_003085.2:n.244T>C
- NR_136154.1:n.249T>C
This HGVS expression did not pass validation- Molecular consequence:
- NM_001322003.2:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001322005.2:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001322007.2:c.-54T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001322009.2:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001322011.2:c.-723T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001322012.2:c.-723T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001322013.2:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001322015.2:c.-323T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406875.1:c.-323T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406876.1:c.-54T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406877.1:c.-323T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406878.1:c.-323T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406880.1:c.-270T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406882.1:c.-323T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406883.1:c.-54T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406887.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406888.1:c.-191T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406889.1:c.-191T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406890.1:c.-234T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406891.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406892.1:c.-191T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406893.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406894.1:c.-191T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406896.1:c.-54T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406897.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406898.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406899.1:c.-191T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406900.1:c.-220T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406901.1:c.-54T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406902.1:c.-54T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406903.1:c.-54T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406904.1:c.-191T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406905.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406906.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406907.1:c.-191T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406908.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406909.1:c.-191T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001406910.1:c.-244T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001322004.2:c.-242-1835T>C - intron variant - [Sequence Ontology: SO:0001627]
- NM_001322008.2:c.-52-1835T>C - intron variant - [Sequence Ontology: SO:0001627]
- NM_001322010.2:c.-242-1835T>C - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406879.1:c.-321-1835T>C - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406881.1:c.-218-1835T>C - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406895.1:c.-189-1835T>C - intron variant - [Sequence Ontology: SO:0001627]
- NM_001406911.1:c.-242-1835T>C - intron variant - [Sequence Ontology: SO:0001627]
- NR_136154.1:n.249T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NM_000535.7:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322006.2:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001322014.2:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406866.1:c.348T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406868.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406869.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406870.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406871.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406872.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406873.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406874.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406884.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406885.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406886.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001406912.1:c.162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
Condition(s)
- Name:
- Hereditary nonpolyposis colorectal neoplasms
- Identifiers:
- MeSH: D003123; MedGen: C0009405
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV004266579 | Invitae | criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) | Uncertain significance (Dec 12, 2023) | germline | clinical testing |
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 |
Citations
PubMed
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.
Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.
- PMID:
- 28492532
- PMCID:
- PMC5632818
Details of each submission
From Invitae, SCV004266579.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This sequence change affects codon 54 of the PMS2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the PMS2 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
# | 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: Feb 20, 2024