NM_000535.7(PMS2):c.1119_1122del (p.Gln374fs) 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:: RCV003453647.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1119_1122del (p.Gln374fs)]

NM_000535.7(PMS2):c.1119_1122del (p.Gln374fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.1119_1122del (p.Gln374fs)

HGVS:

NC_000007.14:g.5989823TGAC[1]
NG_008466.1:g.24278TCAG[1]
NM_000535.5:c.1119_1122del
NM_000535.7:c.1119_1122delMANE SELECT
NM_001322003.2:c.714_717del
NM_001322004.2:c.714_717del
NM_001322005.2:c.714_717del
NM_001322006.2:c.988+2148_988+2151del
NM_001322007.2:c.801_804del
NM_001322008.2:c.801_804del
NM_001322009.2:c.714_717del
NM_001322010.2:c.583+2148_583+2151del
NM_001322011.2:c.186_189del
NM_001322012.2:c.186_189del
NM_001322013.2:c.546_549del
NM_001322014.2:c.1119_1122del
NM_001322015.2:c.810_813del
NP_000526.2:p.Gln374fs
NP_001308932.1:p.Gln239fs
NP_001308933.1:p.Gln239fs
NP_001308934.1:p.Gln239fs
NP_001308936.1:p.Gln268fs
NP_001308937.1:p.Gln268fs
NP_001308938.1:p.Gln239fs
NP_001308940.1:p.Gln63fs
NP_001308941.1:p.Gln63fs
NP_001308942.1:p.Gln183fs
NP_001308943.1:p.Gln374fs
NP_001308944.1:p.Gln271fs
LRG_161t1:c.1119_1122del
LRG_161:g.24278TCAG[1]
NC_000007.13:g.6029453_6029456del
NC_000007.13:g.6029454TGAC[1]
NC_000007.14:g.5989822_5989825delCTGA
NM_000535.5:c.1119_1122delTCAG
NM_000535.7:c.1119_1122del
NR_136154.1:n.1202TCAG[1]

Protein change:

Q183fs

Links:

dbSNP: rs757679199

NCBI 1000 Genomes Browser:

rs757679199

Molecular consequence:

NM_000535.7:c.1119_1122del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.714_717del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.714_717del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.714_717del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.801_804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.801_804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.714_717del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.186_189del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.186_189del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.546_549del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.1119_1122del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.810_813del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.988+2148_988+2151del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.583+2148_583+2151del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.1202TCAG[1] - 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
SCV004188622	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

SCV004188622

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., SCV004188622.1

#	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: Jun 23, 2024

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