NM_000179.3(MSH6):c.4018_4032del (p.Ser1340_Thr1344del) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 9, 2022
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:: RCV000629807.7

Allele description [Variation Report for NM_000179.3(MSH6):c.4018_4032del (p.Ser1340_Thr1344del)]

NM_000179.3(MSH6):c.4018_4032del (p.Ser1340_Thr1344del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.4018_4032del (p.Ser1340_Thr1344del)

HGVS:

NC_000002.12:g.47806795_47806809del
NG_007111.1:g.28649_28663del
NG_008397.1:g.103869_103883del
NM_000179.3:c.4018_4032delMANE SELECT
NM_001281492.2:c.3628_3642del
NM_001281493.2:c.3112_3126del
NM_001281494.2:c.3112_3126del
NP_000170.1:p.Ser1340_Thr1344del
NP_000170.1:p.Ser1340_Thr1344del
NP_001268421.1:p.Ser1210_Thr1214del
NP_001268422.1:p.Ser1038_Thr1042del
NP_001268423.1:p.Ser1038_Thr1042del
LRG_219t1:c.4018_4032del
LRG_219:g.28649_28663del
LRG_219p1:p.Ser1340_Thr1344del
NC_000002.11:g.48033932_48033946del
NC_000002.11:g.48033934_48033948del
NM_000179.2:c.4018_4032del
NM_000179.2:c.4018_4032delAGTGAAAGGTCAACT

Links:

dbSNP: rs1553333998

NCBI 1000 Genomes Browser:

rs1553333998

Molecular consequence:

NM_000179.3:c.4018_4032del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281492.2:c.3628_3642del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281493.2:c.3112_3126del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281494.2:c.3112_3126del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000750763	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 9, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000750763

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 9, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000750763.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 525655). This variant has not been reported in the literature in individuals affected with MSH6-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.4018_4032del, results in the deletion of 5 amino acid(s) of the MSH6 protein (p.Ser1340_Thr1344del), but otherwise preserves the integrity of the reading frame.

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

Last Updated: Sep 29, 2024

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