NM_000535.7(PMS2):c.351del (p.Ser118fs) AND Lynch syndrome 4

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 18, 2023
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:: RCV003455789.1

Allele description [Variation Report for NM_000535.7(PMS2):c.351del (p.Ser118fs)]

NM_000535.7(PMS2):c.351del (p.Ser118fs)

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.351del (p.Ser118fs)

HGVS:

NC_000007.14:g.6003692del
NG_008466.1:g.10415del
NM_000535.7:c.351delMANE SELECT
NM_001018040.1:c.-55delG
NM_001322003.2:c.-55del
NM_001322004.2:c.-55del
NM_001322005.2:c.-55del
NM_001322006.2:c.351del
NM_001322007.2:c.35+280del
NM_001322008.2:c.35+280del
NM_001322009.2:c.-55del
NM_001322010.2:c.-55del
NM_001322011.2:c.-534del
NM_001322012.2:c.-534del
NM_001322013.2:c.-55del
NM_001322014.2:c.351del
NM_001322015.2:c.-134del
NM_001406866.1:c.537del
NM_001406868.1:c.375del
NM_001406869.1:c.351del
NM_001406870.1:c.351del
NM_001406871.1:c.351del
NM_001406872.1:c.351del
NM_001406873.1:c.351del
NM_001406874.1:c.351del
NM_001406875.1:c.-134del
NM_001406876.1:c.35+280del
NM_001406877.1:c.-134del
NM_001406878.1:c.-134del
NM_001406879.1:c.-134del
NM_001406880.1:c.-132+51del
NM_001406881.1:c.-132+280del
NM_001406882.1:c.-134del
NM_001406883.1:c.35+280del
NM_001406884.1:c.351del
NM_001406885.1:c.250+280del
NM_001406886.1:c.351del
NM_001406887.1:c.-55del
NM_001406888.1:c.-53+51del
NM_001406889.1:c.-53+51del
NM_001406890.1:c.-53+8del
NM_001406891.1:c.-55del
NM_001406892.1:c.-53+51del
NM_001406893.1:c.-55del
NM_001406894.1:c.-53+51del
NM_001406895.1:c.-53+51del
NM_001406896.1:c.-52-1056del
NM_001406897.1:c.-55del
NM_001406898.1:c.-55del
NM_001406899.1:c.-53+51del
NM_001406900.1:c.-132+280del
NM_001406901.1:c.35+280del
NM_001406902.1:c.35+280del
NM_001406903.1:c.35+280del
NM_001406904.1:c.-53+51del
NM_001406905.1:c.-55del
NM_001406906.1:c.-55del
NM_001406907.1:c.-53+51del
NM_001406908.1:c.-55del
NM_001406909.1:c.-53+51del
NM_001406910.1:c.-55del
NM_001406911.1:c.-55del
NM_001406912.1:c.351del
NP_000526.1:p.Ser118Alafs
NP_000526.2:p.Ser118fs
NP_001308935.1:p.Ser118fs
NP_001308943.1:p.Ser118fs
NP_001393795.1:p.Ser180fs
NP_001393797.1:p.Ser126fs
NP_001393798.1:p.Ser118fs
NP_001393799.1:p.Ser118fs
NP_001393800.1:p.Ser118fs
NP_001393801.1:p.Ser118fs
NP_001393802.1:p.Ser118fs
NP_001393803.1:p.Ser118fs
NP_001393813.1:p.Ser118fs
NP_001393815.1:p.Ser118fs
NP_001393841.1:p.Ser118fs
LRG_161t1:c.351del
LRG_161:g.10415del
LRG_161p1:p.Ser118Alafs
NC_000007.13:g.6043323del
NM_000535.5:c.351delG
NR_003085.2:n.433delG
NR_136154.1:n.438del

Protein change:

S118fs

Molecular consequence:

NM_001322003.2:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-534del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-534del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-134del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406875.1:c.-134del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406877.1:c.-134del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406878.1:c.-134del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406879.1:c.-134del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406882.1:c.-134del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406887.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406891.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406893.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406897.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406898.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406905.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406906.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406908.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406910.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406911.1:c.-55del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406866.1:c.537del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406868.1:c.375del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406869.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406870.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406871.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406872.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406873.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406874.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406884.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406886.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406912.1:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.35+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406876.1:c.35+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406880.1:c.-132+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406881.1:c.-132+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406883.1:c.35+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406885.1:c.250+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406888.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406889.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406890.1:c.-53+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406892.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406894.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406895.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406896.1:c.-52-1056del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406899.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406900.1:c.-132+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406901.1:c.35+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406902.1:c.35+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406903.1:c.35+280del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406904.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406907.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406909.1:c.-53+51del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.438del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Lynch syndrome 4 (LYNCH4)
Synonyms:: Colorectal cancer, hereditary nonpolyposis, type 4; Hereditary non-polyposis colorectal cancer, type 4
Identifiers:: MONDO: MONDO:0013699; MedGen: C1838333; Orphanet: 144; OMIM: 614337

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004188719	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Sep 18, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004188719

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Sep 18, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV004188719.1

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

Description

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

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

Last Updated: May 1, 2024

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