NM_000535.7(PMS2):c.1117dup (p.Ser373fs) AND Lynch syndrome 4

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 20, 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:: RCV003455151.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1117dup (p.Ser373fs)]

NM_000535.7(PMS2):c.1117dup (p.Ser373fs)

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.1117dup (p.Ser373fs)

HGVS:

NC_000007.14:g.5989827dup
NG_008466.1:g.24280dup
NM_000535.7:c.1117dupMANE SELECT
NM_001322003.2:c.712dup
NM_001322004.2:c.712dup
NM_001322005.2:c.712dup
NM_001322006.2:c.988+2146dup
NM_001322007.2:c.799dup
NM_001322008.2:c.799dup
NM_001322009.2:c.712dup
NM_001322010.2:c.583+2146dup
NM_001322011.2:c.184dup
NM_001322012.2:c.184dup
NM_001322013.2:c.544dup
NM_001322014.2:c.1117dup
NM_001322015.2:c.808dup
NP_000526.2:p.Ser373fs
NP_001308932.1:p.Ser238fs
NP_001308933.1:p.Ser238fs
NP_001308934.1:p.Ser238fs
NP_001308936.1:p.Ser267fs
NP_001308937.1:p.Ser267fs
NP_001308938.1:p.Ser238fs
NP_001308940.1:p.Ser62fs
NP_001308941.1:p.Ser62fs
NP_001308942.1:p.Ser182fs
NP_001308943.1:p.Ser373fs
NP_001308944.1:p.Ser270fs
LRG_161t1:c.1117dup
LRG_161:g.24280dup
NC_000007.13:g.6029457_6029458insT
NC_000007.13:g.6029458dup
NM_000535.5:c.1117dup
NM_000535.5:c.1117dupA
NR_136154.1:n.1204dup

Protein change:

S182fs

Links:

dbSNP: rs1783516106

NCBI 1000 Genomes Browser:

rs1783516106

Molecular consequence:

NM_000535.7:c.1117dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.712dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.712dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.712dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.799dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.799dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.712dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.184dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.184dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.544dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.1117dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.808dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.988+2146dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.583+2146dup - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.1204dup - 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
SCV004188707	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Sep 20, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004188707

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Sep 20, 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., SCV004188707.1

#	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: Sep 29, 2024

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