NM_000535.7(PMS2):c.2041del (p.Gln681fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 22, 2020
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:: RCV002419945.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2041del (p.Gln681fs)]

NM_000535.7(PMS2):c.2041del (p.Gln681fs)

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.2041del (p.Gln681fs)

HGVS:

NC_000007.14:g.5982957del
NG_008466.1:g.31150del
NM_000535.7:c.2041delMANE SELECT
NM_001018040.1:c.1636delC
NM_001322003.2:c.1636del
NM_001322004.2:c.1636del
NM_001322005.2:c.1636del
NM_001322006.2:c.1885del
NM_001322007.2:c.1723del
NM_001322008.2:c.1723del
NM_001322009.2:c.1636del
NM_001322010.2:c.1480del
NM_001322011.2:c.1108del
NM_001322012.2:c.1108del
NM_001322013.2:c.1468del
NM_001322014.2:c.2041del
NM_001322015.2:c.1732del
NM_001406866.1:c.2227delC
NM_001406868.1:c.2065delC
NM_001406869.1:c.1933delC
NM_001406870.1:c.1885delC
NM_001406871.1:c.2041delC
NM_001406873.1:c.1843delC
NM_001406874.1:c.1873delC
NM_001406875.1:c.1732delC
NM_001406876.1:c.1723delC
NM_001406877.1:c.1732delC
NM_001406878.1:c.1732delC
NM_001406879.1:c.1732delC
NM_001406880.1:c.1732delC
NM_001406881.1:c.1732delC
NM_001406882.1:c.1732delC
NM_001406883.1:c.1723delC
NM_001406884.1:c.1717delC
NM_001406885.1:c.1705delC
NM_001406886.1:c.1675delC
NM_001406887.1:c.1636delC
NM_001406888.1:c.1636delC
NM_001406889.1:c.1636delC
NM_001406890.1:c.1636delC
NM_001406891.1:c.1636delC
NM_001406892.1:c.1636delC
NM_001406893.1:c.1636delC
NM_001406894.1:c.1636delC
NM_001406895.1:c.1636delC
NM_001406896.1:c.1636delC
NM_001406897.1:c.1636delC
NM_001406898.1:c.1636delC
NM_001406899.1:c.1636delC
NM_001406900.1:c.1576delC
NM_001406901.1:c.1567delC
NM_001406902.1:c.1567delC
NM_001406904.1:c.1528delC
NM_001406905.1:c.1528delC
NM_001406906.1:c.1480delC
NM_001406907.1:c.1480delC
NM_001406909.1:c.1468delC
NM_001406911.1:c.1270delC
NM_001406912.1:c.838delC
NP_000526.1:p.Gln681Serfs
NP_000526.2:p.Gln681fs
NP_001018050.1:p.Gln546Serfs
NP_001308932.1:p.Gln546fs
NP_001308933.1:p.Gln546fs
NP_001308934.1:p.Gln546fs
NP_001308935.1:p.Gln629fs
NP_001308936.1:p.Gln575fs
NP_001308937.1:p.Gln575fs
NP_001308938.1:p.Gln546fs
NP_001308939.1:p.Gln494fs
NP_001308940.1:p.Gln370fs
NP_001308941.1:p.Gln370fs
NP_001308942.1:p.Gln490fs
NP_001308943.1:p.Gln681fs
NP_001308944.1:p.Gln578fs
NP_001393795.1:p.Gln743Serfs
NP_001393797.1:p.Gln689Serfs
NP_001393798.1:p.Gln645Serfs
NP_001393799.1:p.Gln629Serfs
NP_001393800.1:p.Gln681Serfs
NP_001393802.1:p.Gln615Serfs
NP_001393803.1:p.Gln625Serfs
NP_001393804.1:p.Gln578Serfs
NP_001393805.1:p.Gln575Serfs
NP_001393806.1:p.Gln578Serfs
NP_001393807.1:p.Gln578Serfs
NP_001393808.1:p.Gln578Serfs
NP_001393809.1:p.Gln578Serfs
NP_001393810.1:p.Gln578Serfs
NP_001393811.1:p.Gln578Serfs
NP_001393812.1:p.Gln575Serfs
NP_001393813.1:p.Gln573Serfs
NP_001393814.1:p.Gln569Serfs
NP_001393815.1:p.Gln559Serfs
NP_001393816.1:p.Gln546Serfs
NP_001393817.1:p.Gln546Serfs
NP_001393818.1:p.Gln546Serfs
NP_001393819.1:p.Gln546Serfs
NP_001393820.1:p.Gln546Serfs
NP_001393821.1:p.Gln546Serfs
NP_001393822.1:p.Gln546Serfs
NP_001393823.1:p.Gln546Serfs
NP_001393824.1:p.Gln546Serfs
NP_001393825.1:p.Gln546Serfs
NP_001393826.1:p.Gln546Serfs
NP_001393827.1:p.Gln546Serfs
NP_001393828.1:p.Gln546Serfs
NP_001393829.1:p.Gln526Serfs
NP_001393830.1:p.Gln523Serfs
NP_001393831.1:p.Gln523Serfs
NP_001393833.1:p.Gln510Serfs
NP_001393834.1:p.Gln510Serfs
NP_001393835.1:p.Gln494Serfs
NP_001393836.1:p.Gln494Serfs
NP_001393838.1:p.Gln490Serfs
NP_001393840.1:p.Gln424Serfs
NP_001393841.1:p.Gln280Serfs
LRG_161t1:c.2041del
LRG_161:g.31150del
LRG_161p1:p.Gln681Serfs
NC_000007.13:g.6022588del
NM_000535.5:c.2041delC
NR_003085.2:n.2123delC
NR_136154.1:n.2128del

Protein change:

Q370fs

Molecular consequence:

NM_000535.7:c.2041del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001018040.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.1636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.1636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.1636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.1885del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.1723del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.1723del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.1636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322010.2:c.1480del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.1108del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.1108del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.1468del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.2041del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.1732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406866.1:c.2227delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406868.1:c.2065delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406869.1:c.1933delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406870.1:c.1885delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406871.1:c.2041delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406873.1:c.1843delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406874.1:c.1873delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406875.1:c.1732delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406876.1:c.1723delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406877.1:c.1732delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406878.1:c.1732delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406879.1:c.1732delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406880.1:c.1732delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406881.1:c.1732delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406882.1:c.1732delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406883.1:c.1723delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406884.1:c.1717delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406885.1:c.1705delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406886.1:c.1675delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406887.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406888.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406889.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406890.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406891.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406892.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406893.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406894.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406895.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406896.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406897.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406898.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406899.1:c.1636delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406900.1:c.1576delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406901.1:c.1567delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406902.1:c.1567delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406904.1:c.1528delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406905.1:c.1528delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406906.1:c.1480delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406907.1:c.1480delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406909.1:c.1468delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406911.1:c.1270delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406912.1:c.838delC - frameshift variant - [Sequence Ontology: SO:0001589]
NR_136154.1:n.2128del - 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
SCV002719803	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (May 22, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002719803

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(May 22, 2020)

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, SCV002719803.2

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

Description

The c.2041delC pathogenic mutation, located in coding exon 12 of the PMS2 gene, results from a deletion of one nucleotide at nucleotide position 2041, causing a translational frameshift with a predicted alternate stop codon (p.Q681Sfs*7). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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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