NM_000535.7(PMS2):c.104_106dup (p.Leu35_Ser36insIle) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 4, 2021
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:: RCV002389772.2

Allele description [Variation Report for NM_000535.7(PMS2):c.104_106dup (p.Leu35_Ser36insIle)]

NM_000535.7(PMS2):c.104_106dup (p.Leu35_Ser36insIle)

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.104_106dup (p.Leu35_Ser36insIle)

HGVS:

NC_000007.14:g.6005949_6005951dup
NG_008466.1:g.8156_8158dup
NG_050738.1:g.1699_1701dup
NM_000535.7:c.104_106dupMANE SELECT
NM_001018040.1:c.-302_-300dup
NM_001322003.2:c.-302_-300dup
NM_001322004.2:c.-242-1893_-242-1891dup
NM_001322005.2:c.-302_-300dup
NM_001322006.2:c.104_106dup
NM_001322007.2:c.-112_-110dup
NM_001322008.2:c.-52-1893_-52-1891dup
NM_001322009.2:c.-302_-300dup
NM_001322010.2:c.-242-1893_-242-1891dup
NM_001322011.2:c.-781_-779dup
NM_001322012.2:c.-781_-779dup
NM_001322013.2:c.-302_-300dup
NM_001322014.2:c.104_106dup
NM_001322015.2:c.-381_-379dup
NM_001406866.1:c.290_292dup
NM_001406868.1:c.104_106dup
NM_001406869.1:c.104_106dup
NM_001406870.1:c.104_106dup
NM_001406871.1:c.104_106dup
NM_001406872.1:c.104_106dup
NM_001406873.1:c.104_106dup
NM_001406874.1:c.104_106dup
NM_001406875.1:c.-381_-379dup
NM_001406876.1:c.-112_-110dup
NM_001406877.1:c.-381_-379dup
NM_001406878.1:c.-381_-379dup
NM_001406880.1:c.-328_-326dup
NM_001406882.1:c.-381_-379dup
NM_001406883.1:c.-112_-110dup
NM_001406884.1:c.104_106dup
NM_001406885.1:c.104_106dup
NM_001406886.1:c.104_106dup
NM_001406887.1:c.-302_-300dup
NM_001406888.1:c.-249_-247dup
NM_001406889.1:c.-249_-247dup
NM_001406890.1:c.-292_-290dup
NM_001406891.1:c.-302_-300dup
NM_001406892.1:c.-249_-247dup
NM_001406893.1:c.-302_-300dup
NM_001406894.1:c.-249_-247dup
NM_001406896.1:c.-112_-110dup
NM_001406897.1:c.-302_-300dup
NM_001406898.1:c.-302_-300dup
NM_001406899.1:c.-249_-247dup
NM_001406900.1:c.-278_-276dup
NM_001406901.1:c.-112_-110dup
NM_001406902.1:c.-112_-110dup
NM_001406903.1:c.-112_-110dup
NM_001406904.1:c.-249_-247dup
NM_001406905.1:c.-302_-300dup
NM_001406906.1:c.-302_-300dup
NM_001406907.1:c.-249_-247dup
NM_001406908.1:c.-302_-300dup
NM_001406909.1:c.-249_-247dup
NM_001406910.1:c.-302_-300dup
NM_001406912.1:c.104_106dup
NP_000526.1:p.Leu35_Ser36insIle
NP_000526.2:p.Leu35_Ser36insIle
NP_001308935.1:p.Leu35_Ser36insIle
NP_001308943.1:p.Leu35_Ser36insIle
NP_001393795.1:p.Leu97_Ser98insIle
NP_001393797.1:p.Leu35_Ser36insIle
NP_001393798.1:p.Leu35_Ser36insIle
NP_001393799.1:p.Leu35_Ser36insIle
NP_001393800.1:p.Leu35_Ser36insIle
NP_001393801.1:p.Leu35_Ser36insIle
NP_001393802.1:p.Leu35_Ser36insIle
NP_001393803.1:p.Leu35_Ser36insIle
NP_001393813.1:p.Leu35_Ser36insIle
NP_001393814.1:p.Leu35_Ser36insIle
NP_001393815.1:p.Leu35_Ser36insIle
NP_001393841.1:p.Leu35_Ser36insIle
LRG_161t1:c.104_106dup
LRG_161:g.8156_8158dup
LRG_161p1:p.Leu35_Ser36insIle
NC_000007.13:g.6045580_6045582dup
NM_000535.5:c.104_106dup
NM_000535.5:c.104_106dupTAA
NR_003085.2:n.186_188dup
NR_136154.1:n.191_193dup

Molecular consequence:

NM_001322003.2:c.-302_-300dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-302_-300dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-112_-110dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-302_-300dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-781_-779dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-781_-779dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-302_-300dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-381_-379dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406866.1:c.290_292dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406868.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406869.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406870.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406871.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406872.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406873.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406874.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406884.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406885.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406886.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406912.1:c.104_106dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_000535.7:c.104_106dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001322006.2:c.104_106dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001322014.2:c.104_106dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001322004.2:c.-242-1893_-242-1891dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1893_-52-1891dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1893_-242-1891dup - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.191_193dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002700488	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 4, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002700488

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 4, 2021)

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, SCV002700488.2

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

Description

The c.104_106dupTAA variant (also known as p.L35_S36insI), located in coding exon 2 of the PMS2 gene, results from an in-frame duplication of TAA at nucleotide positions 104 to 106. This results in the insertion of one residue between codons 35 and 36. This amino acid region is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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