NM_000179.3(MSH6):c.3528_3532del (p.Leu1177fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 22, 2021
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:: RCV000202131.9

Allele description [Variation Report for NM_000179.3(MSH6):c.3528_3532del (p.Leu1177fs)]

NM_000179.3(MSH6):c.3528_3532del (p.Leu1177fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3528_3532del (p.Leu1177fs)

HGVS:

NC_000002.12:g.47804999_47805003del
NG_007111.1:g.26853_26857del
NG_008397.1:g.105674_105678del
NM_000179.3:c.3528_3532delMANE SELECT
NM_001281492.2:c.3138_3142del
NM_001281493.2:c.2622_2626del
NM_001281494.2:c.2622_2626del
NP_000170.1:p.Leu1177fs
NP_000170.1:p.Leu1177fs
NP_001268421.1:p.Leu1047fs
NP_001268422.1:p.Leu875fs
NP_001268423.1:p.Leu875fs
LRG_219t1:c.3528_3532del
LRG_219:g.26853_26857del
LRG_219p1:p.Leu1177fs
NC_000002.11:g.48032137_48032141del
NC_000002.11:g.48032138_48032142del
NM_000179.2:c.3528_3532del
NM_000179.2:c.3528_3532delACTTG

Protein change:

L1047fs

Links:

dbSNP: rs863225408

NCBI 1000 Genomes Browser:

rs863225408

Molecular consequence:

NM_000179.3:c.3528_3532del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.3138_3142del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.2622_2626del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.2622_2626del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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hypothetical protein CC31p261 [Enterobacter phage CC31]
hypothetical protein CC31p261 [Enterobacter phage CC31]
gi|311993253|ref|YP_004010119.1|

Protein
PREDICTED: Homo sapiens TBC1 domain family member 10C (TBC1D10C), transcript var...
PREDICTED: Homo sapiens TBC1 domain family member 10C (TBC1D10C), transcript variant X4, mRNA
gi|2462525060|ref|XM_054368709.1|

Nucleotide
carabin isoform 4 [Homo sapiens]
carabin isoform 4 [Homo sapiens]
gi|1610575763|ref|NP_001356423.1|

Protein
carabin isoform X2 [Homo sapiens]
carabin isoform X2 [Homo sapiens]
gi|2462525059|ref|XP_054224683.1|

Protein
Tssr124518 AND (alive[prop]) (0)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000257262	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Likely pathogenic	unknown	research
SCV000568728	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 22, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000257262

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Likely pathogenic

unknown

research

SCV000568728

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jun 22, 2021)

germline

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	1	not provided	not provided	not provided	not provided	research
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV000257262.1

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

#	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		1	not provided	not provided	not provided

From GeneDx, SCV000568728.4

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (Lek 2016); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Observed in families with Lynch syndrome (Baglietto 2010); This variant is associated with the following publications: (PMID: 22949379, 20028993, 27535533)

#	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		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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