NM_000179.3(MSH6):c.878_883delinsTTCG (p.Pro293fs) AND Lynch syndrome 5

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 11, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001523829.2

Allele description [Variation Report for NM_000179.3(MSH6):c.878_883delinsTTCG (p.Pro293fs)]

NM_000179.3(MSH6):c.878_883delinsTTCG (p.Pro293fs)

Gene:

MSH6:mutS homolog 6 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.878_883delinsTTCG (p.Pro293fs)

HGVS:

NC_000002.12:g.47798861_47798866delinsTTCG
NG_007111.1:g.20715_20720delinsTTCG
NM_000179.3:c.878_883delinsTTCGMANE SELECT
NM_001281492.2:c.488_493delinsTTCG
NM_001281493.2:c.-29_-24delinsTTCG
NM_001281494.2:c.-29_-24delinsTTCG
NP_000170.1:p.Pro293fs
NP_001268421.1:p.Pro163fs
LRG_219:g.20715_20720delinsTTCG
NC_000002.11:g.48026000_48026005delinsTTCG
NM_000179.2:c.878_883delCTGTCAinsTTCG
NM_000179.3:c.878_883delinsTTCG

Protein change:

P163fs

Links:

dbSNP: rs1114167748

NCBI 1000 Genomes Browser:

rs1114167748

Molecular consequence:

NM_001281493.2:c.-29_-24delinsTTCG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001281494.2:c.-29_-24delinsTTCG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000179.3:c.878_883delinsTTCG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.488_493delinsTTCG - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Lynch syndrome 5 (LYNCH5)
Synonyms:: Colorectal cancer, hereditary nonpolyposis, type 5; Hereditary non-polyposis colorectal cancer, type 5
Identifiers:: MONDO: MONDO:0013710; MedGen: C1833477; Orphanet: 144; OMIM: 614350

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001478128	Department of Pediatrics, Memorial Sloan Kettering Cancer Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 15, 2020)	germline	research	PubMed (2) [See all records that cite these PMIDs] 28873162, 25741868
SCV004185767	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Aug 11, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001478128

Department of Pediatrics, Memorial Sloan Kettering Cancer Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 15, 2020)

germline

research

PubMed (2)
[See all records that cite these PMIDs]

SCV004185767

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Aug 11, 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
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing.

Mandelker D, Zhang L, Kemel Y, Stadler ZK, Joseph V, Zehir A, Pradhan N, Arnold A, Walsh MF, Li Y, Balakrishnan AR, Syed A, Prasad M, Nafa K, Carlo MI, Cadoo KA, Sheehan M, Fleischut MH, Salo-Mullen E, Trottier M, Lipkin SM, Lincoln A, et al.

JAMA. 2017 Sep 5;318(9):825-835. doi: 10.1001/jama.2017.11137. Erratum in: JAMA. 2018 Dec 11;320(22):2381. doi: 10.1001/jama.2018.17511.

PubMed [citation]

PMID:: 28873162
PMCID:: PMC5611881

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Department of Pediatrics, Memorial Sloan Kettering Cancer Center, SCV001478128.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Myriad Genetics, Inc., SCV004185767.1

#	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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