NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs) AND Lynch syndrome 5

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Mar 30, 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:: RCV000576542.4

Allele description [Variation Report for NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs)]

NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs)

HGVS:

NC_000002.12:g.47806256_47806259del
NG_007111.1:g.28110_28113del
NG_008397.1:g.104419_104422del
NM_000179.3:c.3699_3702delMANE SELECT
NM_001281492.2:c.3309_3312del
NM_001281493.2:c.2793_2796del
NM_001281494.2:c.2793_2796del
NP_000170.1:p.Lys1233fs
NP_001268421.1:p.Lys1103fs
NP_001268422.1:p.Lys931fs
NP_001268423.1:p.Lys931fs
LRG_219:g.28110_28113del
NC_000002.11:g.48033393_48033396del
NC_000002.11:g.48033395_48033398del
NM_000179.2:c.3699_3702delAGAA
NM_000179.3:c.3699_3702del
p.K1233NFS*6
p.Lys1233Asnfs*6
p.Lys1233AsnfsX6

Protein change:

K1103fs

Links:

dbSNP: rs193922343

NCBI 1000 Genomes Browser:

rs193922343

Molecular consequence:

NM_000179.3:c.3699_3702del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.3309_3312del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.2793_2796del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.2793_2796del - 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
SCV000677728	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Pathogenic (Jun 3, 2015)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18389388, 21642682, 25980754 Citation Link,
SCV002515807	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - HudsonAlpha-AGHI-WGS	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 24, 2021)	unknown	research	PubMed (1) [See all records that cite this PMID]
SCV004019085	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Mar 30, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000677728

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Pathogenic
(Jun 3, 2015)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV002515807

HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - HudsonAlpha-AGHI-WGS

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 24, 2021)

unknown

research

PubMed (1)
[See all records that cite this PMID]

SCV004019085

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Mar 30, 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	yes	1	not provided	not provided	1	not provided	research
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutation spectrum in HNPCC in the Israeli population.

Goldberg Y, Porat RM, Kedar I, Shochat C, Sagi M, Eilat A, Mendelson S, Hamburger T, Nissan A, Hubert A, Kadouri L, Pikarski E, Lerer I, Abeliovich D, Bercovich D, Peretz T.

Fam Cancer. 2008;7(4):309-17. doi: 10.1007/s10689-008-9191-y. Epub 2008 Apr 4.

PubMed [citation]

PMID:: 18389388

Cancer risks associated with germline mutations in MLH1, MSH2, and MSH6 genes in Lynch syndrome.

Bonadona V, Bonaïti B, Olschwang S, Grandjouan S, Huiart L, Longy M, Guimbaud R, Buecher B, Bignon YJ, Caron O, Colas C, Noguès C, Lejeune-Dumoulin S, Olivier-Faivre L, Polycarpe-Osaer F, Nguyen TD, Desseigne F, Saurin JC, Berthet P, Leroux D, Duffour J, Manouvrier S, et al.

JAMA. 2011 Jun 8;305(22):2304-10. doi: 10.1001/jama.2011.743.

PubMed [citation]

PMID:: 21642682

See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000677728.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

#	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

From HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - HudsonAlpha-AGHI-WGS, SCV002515807.1

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

Description

ACMG codes: PVS1, PS4M, PM2, PP5

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

From Myriad Genetics, Inc., SCV004019085.1

#	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: Nov 24, 2024

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