NM_000179.3(MSH6):c.3845_3847del (p.Thr1282del) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 14, 2023
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:: RCV000697631.10

Allele description [Variation Report for NM_000179.3(MSH6):c.3845_3847del (p.Thr1282del)]

NM_000179.3(MSH6):c.3845_3847del (p.Thr1282del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3845_3847del (p.Thr1282del)

HGVS:

NC_000002.12:g.47806495_47806497del
NG_007111.1:g.28349_28351del
NG_008397.1:g.104180_104182del
NM_000179.3:c.3845_3847delMANE SELECT
NM_001281492.2:c.3455_3457del
NM_001281493.2:c.2939_2941del
NM_001281494.2:c.2939_2941del
NP_000170.1:p.Thr1282del
NP_000170.1:p.Thr1282del
NP_001268421.1:p.Thr1152del
NP_001268422.1:p.Thr980del
NP_001268423.1:p.Thr980del
LRG_219t1:c.3845_3847del
LRG_219:g.28349_28351del
LRG_219p1:p.Thr1282del
NC_000002.11:g.48033633_48033635del
NC_000002.11:g.48033634_48033636del
NM_000179.2:c.3845_3847del
NM_000179.2:c.3845_3847delCTA

Protein change:

T1152del

Links:

dbSNP: rs1367615271

NCBI 1000 Genomes Browser:

rs1367615271

Molecular consequence:

NM_000179.3:c.3845_3847del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281492.2:c.3455_3457del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281493.2:c.2939_2941del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281494.2:c.2939_2941del - 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
SCV000826253	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 14, 2023)	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

SCV000826253

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 14, 2023)

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, SCV000826253.7

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

Description

This variant, c.3845_3847del, results in the deletion of 1 amino acid(s) of the MSH6 protein (p.Thr1282del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MSH6-related conditions. ClinVar contains an entry for this variant (Variation ID: 490010). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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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