NM_000535.7(PMS2):c.1957del (p.Cys653fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 7, 2018
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:: RCV002421643.2

Allele description [Variation Report for NM_000535.7(PMS2):c.1957del (p.Cys653fs)]

NM_000535.7(PMS2):c.1957del (p.Cys653fs)

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.1957del (p.Cys653fs)

HGVS:

NC_000007.14:g.5986810del
NG_008466.1:g.27299del
NM_000535.7:c.1957delMANE SELECT
NM_001018040.1:c.1550delT
NM_001322003.2:c.1552del
NM_001322004.2:c.1552del
NM_001322005.2:c.1552del
NM_001322006.2:c.1801del
NM_001322007.2:c.1639del
NM_001322008.2:c.1639del
NM_001322009.2:c.1552del
NM_001322010.2:c.1396del
NM_001322011.2:c.1024del
NM_001322012.2:c.1024del
NM_001322013.2:c.1384del
NM_001322014.2:c.1957del
NM_001322015.2:c.1648del
NM_001406866.1:c.2141delT
NM_001406868.1:c.1979delT
NM_001406869.1:c.1847delT
NM_001406870.1:c.1799delT
NM_001406871.1:c.1955delT
NM_001406872.1:c.1955delT
NM_001406873.1:c.1757delT
NM_001406874.1:c.1787delT
NM_001406875.1:c.1646delT
NM_001406876.1:c.1637delT
NM_001406877.1:c.1646delT
NM_001406878.1:c.1646delT
NM_001406879.1:c.1646delT
NM_001406880.1:c.1646delT
NM_001406881.1:c.1646delT
NM_001406882.1:c.1646delT
NM_001406883.1:c.1637delT
NM_001406884.1:c.1631delT
NM_001406885.1:c.1619delT
NM_001406886.1:c.1589delT
NM_001406887.1:c.1550delT
NM_001406888.1:c.1550delT
NM_001406889.1:c.1550delT
NM_001406890.1:c.1550delT
NM_001406891.1:c.1550delT
NM_001406892.1:c.1550delT
NM_001406893.1:c.1550delT
NM_001406894.1:c.1550delT
NM_001406895.1:c.1550delT
NM_001406896.1:c.1550delT
NM_001406897.1:c.1550delT
NM_001406898.1:c.1550delT
NM_001406899.1:c.1550delT
NM_001406900.1:c.1490delT
NM_001406901.1:c.1481delT
NM_001406902.1:c.1481delT
NM_001406903.1:c.1637delT
NM_001406904.1:c.1442delT
NM_001406905.1:c.1442delT
NM_001406906.1:c.1394delT
NM_001406907.1:c.1394delT
NM_001406908.1:c.1550delT
NM_001406909.1:c.1382delT
NM_001406910.1:c.1550delT
NM_001406911.1:c.1184delT
NP_000526.1:p.Cys653Valfs
NP_000526.2:p.Cys653fs
NP_001018050.1:p.Cys518Valfs
NP_001308932.1:p.Cys518fs
NP_001308933.1:p.Cys518fs
NP_001308934.1:p.Cys518fs
NP_001308935.1:p.Cys601fs
NP_001308936.1:p.Cys547fs
NP_001308937.1:p.Cys547fs
NP_001308938.1:p.Cys518fs
NP_001308939.1:p.Cys466fs
NP_001308940.1:p.Cys342fs
NP_001308941.1:p.Cys342fs
NP_001308942.1:p.Cys462fs
NP_001308943.1:p.Cys653fs
NP_001308944.1:p.Cys550fs
NP_001393795.1:p.Cys715Valfs
NP_001393797.1:p.Cys661Valfs
NP_001393798.1:p.Cys617Valfs
NP_001393799.1:p.Cys601Valfs
NP_001393800.1:p.Cys653Valfs
NP_001393801.1:p.Cys653Valfs
NP_001393802.1:p.Cys587Valfs
NP_001393803.1:p.Cys597Valfs
NP_001393804.1:p.Cys550Valfs
NP_001393805.1:p.Cys547Valfs
NP_001393806.1:p.Cys550Valfs
NP_001393807.1:p.Cys550Valfs
NP_001393808.1:p.Cys550Valfs
NP_001393809.1:p.Cys550Valfs
NP_001393810.1:p.Cys550Valfs
NP_001393811.1:p.Cys550Valfs
NP_001393812.1:p.Cys547Valfs
NP_001393813.1:p.Cys545Valfs
NP_001393814.1:p.Cys541Valfs
NP_001393815.1:p.Cys531Valfs
NP_001393816.1:p.Cys518Valfs
NP_001393817.1:p.Cys518Valfs
NP_001393818.1:p.Cys518Valfs
NP_001393819.1:p.Cys518Valfs
NP_001393820.1:p.Cys518Valfs
NP_001393821.1:p.Cys518Valfs
NP_001393822.1:p.Cys518Valfs
NP_001393823.1:p.Cys518Valfs
NP_001393824.1:p.Cys518Valfs
NP_001393825.1:p.Cys518Valfs
NP_001393826.1:p.Cys518Valfs
NP_001393827.1:p.Cys518Valfs
NP_001393828.1:p.Cys518Valfs
NP_001393829.1:p.Cys498Valfs
NP_001393830.1:p.Cys495Valfs
NP_001393831.1:p.Cys495Valfs
NP_001393832.1:p.Cys547Valfs
NP_001393833.1:p.Cys482Valfs
NP_001393834.1:p.Cys482Valfs
NP_001393835.1:p.Cys466Valfs
NP_001393836.1:p.Cys466Valfs
NP_001393837.1:p.Cys518Valfs
NP_001393838.1:p.Cys462Valfs
NP_001393839.1:p.Cys518Valfs
NP_001393840.1:p.Cys396Valfs
LRG_161t1:c.1955del
LRG_161:g.27299del
LRG_161p1:p.Cys653Valfs
NC_000007.13:g.6026439del
NC_000007.13:g.6026441del
NM_000535.5:c.1955delT
NM_000535.5:c.1957delT
NR_003085.2:n.2037delT
NR_136154.1:n.2044del

Protein change:

C342fs

Molecular consequence:

NM_000535.7:c.1957del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001018040.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.1552del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.1552del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.1552del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.1801del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.1639del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.1639del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.1552del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322010.2:c.1396del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.1024del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.1024del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.1384del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.1957del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.1648del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406866.1:c.2141delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406868.1:c.1979delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406869.1:c.1847delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406870.1:c.1799delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406871.1:c.1955delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406872.1:c.1955delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406873.1:c.1757delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406874.1:c.1787delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406875.1:c.1646delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406876.1:c.1637delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406877.1:c.1646delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406878.1:c.1646delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406879.1:c.1646delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406880.1:c.1646delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406881.1:c.1646delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406882.1:c.1646delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406883.1:c.1637delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406884.1:c.1631delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406885.1:c.1619delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406886.1:c.1589delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406887.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406888.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406889.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406890.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406891.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406892.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406893.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406894.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406895.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406896.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406897.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406898.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406899.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406900.1:c.1490delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406901.1:c.1481delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406902.1:c.1481delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406903.1:c.1637delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406904.1:c.1442delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406905.1:c.1442delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406906.1:c.1394delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406907.1:c.1394delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406908.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406909.1:c.1382delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406910.1:c.1550delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406911.1:c.1184delT - frameshift variant - [Sequence Ontology: SO:0001589]
NR_136154.1:n.2044del - 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

Recent activity

Clear Turn Off Turn On

adenine phosphoribosyltransferase isoform a [Homo sapiens]
adenine phosphoribosyltransferase isoform a [Homo sapiens]
gi|4502171|ref|NP_000476.1|

Protein
Homo sapiens 5-hydroxytryptamine receptor 3 subunit E (HTR3E), transcript varian...
Homo sapiens 5-hydroxytryptamine receptor 3 subunit E (HTR3E), transcript variant 2, mRNA
gi|45356152|ref|NM_198314.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002722074	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Sep 7, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002722074

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Sep 7, 2018)

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, SCV002722074.2

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

Description

The c.1957delT pathogenic mutation, located in coding exon 11 of the PMS2 gene, results from a deletion of one nucleotide at nucleotide position 1957, causing a translational frameshift with a predicted alternate stop codon (p.C653Vfs*12). 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 7, 2024

ClinVar

Relating variation to medicine