NM_000179.3(MSH6):c.3513_3514del (p.Asp1171fs) AND Lynch syndrome 5

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 24, 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:: RCV002288563.3

Allele description [Variation Report for NM_000179.3(MSH6):c.3513_3514del (p.Asp1171fs)]

NM_000179.3(MSH6):c.3513_3514del (p.Asp1171fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3513_3514del (p.Asp1171fs)

HGVS:

NC_000002.11:g.48032122_48032123del
NC_000002.12:g.47804984_47804985del
NG_007111.1:g.26838_26839del
NG_008397.1:g.105692_105693del
NM_000179.3:c.3513_3514delMANE SELECT
NM_001281492.2:c.3123_3124del
NM_001281493.2:c.2607_2608del
NM_001281494.2:c.2607_2608del
NP_000170.1:p.Asp1171fs
NP_001268421.1:p.Asp1041fs
NP_001268422.1:p.Asp869fs
NP_001268423.1:p.Asp869fs
LRG_219:g.26838_26839del
NC_000002.11:g.48032122_48032123del
NC_000002.11:g.48032123_48032124del
NC_000002.11:g.48032123_48032124delTA
NM_000179.2:c.3513_3514delTA
p.Asp1171Glufs*5
p.Asp1171GlufsX5
p.D1171Efs*5

Protein change:

D1041fs

Links:

dbSNP: rs63750194

NCBI 1000 Genomes Browser:

rs63750194

Molecular consequence:

NM_000179.3:c.3513_3514del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.3123_3124del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.2607_2608del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.2607_2608del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

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
SCV002580256	MGZ Medical Genetics Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 8, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004188206	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Aug 24, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002580256

MGZ Medical Genetics Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 8, 2021)

germline

clinical testing

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

SCV004188206

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Aug 24, 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	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 MGZ Medical Genetics Center, SCV002580256.1

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

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

From Myriad Genetics, Inc., SCV004188206.1

#	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: Oct 8, 2024

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