NM_000179.3(MSH6):c.3556+1del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 14, 2015
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:: RCV000480410.1

Allele description [Variation Report for NM_000179.3(MSH6):c.3556+1del]

NM_000179.3(MSH6):c.3556+1del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3556+1del

HGVS:

NC_000002.12:g.47805028del
NG_007111.1:g.26882del
NG_008397.1:g.105649del
NM_000179.3:c.3556+1delMANE SELECT
NM_001281492.2:c.3166+1del
NM_001281493.2:c.2650+1del
NM_001281494.2:c.2650+1del
NM_001406795.1:c.3652+1del
NM_001406796.1:c.3556+1del
NM_001406797.1:c.3259+1del
NM_001406798.1:c.3382+1del
NM_001406799.1:c.3031+1del
NM_001406800.1:c.3556+1del
NM_001406801.1:c.3259+1del
NM_001406802.1:c.3652+1del
NM_001406803.1:c.2692+1del
NM_001406804.1:c.3478+1del
NM_001406805.1:c.3259+1del
NM_001406806.1:c.3031+1del
NM_001406807.1:c.3031+1del
NM_001406808.1:c.3556+1del
NM_001406809.1:c.3556+1del
NM_001406811.1:c.2650+1del
NM_001406812.1:c.2650+1del
NM_001406813.1:c.3562+1del
NM_001406814.1:c.2650+1del
NM_001406815.1:c.2650+1del
NM_001406816.1:c.2650+1del
NM_001406817.1:c.1990+1del
NM_001406818.1:c.3259+1del
NM_001406819.1:c.3259+1del
NM_001406820.1:c.3259+1del
NM_001406821.1:c.3259+1del
NM_001406822.1:c.3259+1del
NM_001406823.1:c.2650+1del
NM_001406824.1:c.3259+1del
NM_001406825.1:c.3259+1del
NM_001406826.1:c.3388+1del
NM_001406827.1:c.3259+1del
NM_001406828.1:c.3259+1del
NM_001406829.1:c.2650+1del
NM_001406830.1:c.3259+1del
NM_001406831.1:c.337+1del
NM_001406832.1:c.403+1del
NM_001407362.1:c.1501+1del
LRG_219:g.26882del
NC_000002.11:g.48032166del
NC_000002.11:g.48032167del
NM_000179.2:c.3556+1delG

Links:

dbSNP: rs1064793489

NCBI 1000 Genomes Browser:

rs1064793489

Molecular consequence:

NM_000179.3:c.3556+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001281492.2:c.3166+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001281493.2:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001281494.2:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406795.1:c.3652+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406796.1:c.3556+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406797.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406798.1:c.3382+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406799.1:c.3031+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406800.1:c.3556+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406801.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406802.1:c.3652+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406803.1:c.2692+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406804.1:c.3478+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406805.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406806.1:c.3031+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406807.1:c.3031+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406808.1:c.3556+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406809.1:c.3556+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406811.1:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406812.1:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406813.1:c.3562+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406814.1:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406815.1:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406816.1:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406817.1:c.1990+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406818.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406819.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406820.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406821.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406822.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406823.1:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406824.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406825.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406826.1:c.3388+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406827.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406828.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406829.1:c.2650+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406830.1:c.3259+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406831.1:c.337+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406832.1:c.403+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407362.1:c.1501+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566246	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Apr 14, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000566246

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Apr 14, 2015)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000566246.3

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

Description

This pathogenic variant is denoted MSH6 IVS6+1delG or c.3556+1delG and consists of a deletion of one nucleotide at the +1 position of intron 6. The normal sequence, with the base that is deleted in brackets, is TCAG[g]tgag, where the capital letters are exonic and lowercase are intronic. The variant destroys a canonical splice donor site and is predicted to cause abnormal gene splicing, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. This variant has not, to our knowledge, been published in the literature. Based on the currently available information, we consider MSH6 c.3556+1delG to be a pathogenic variant.

#	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: Jun 17, 2024

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