NM_000251.3(MSH2):c.2536_2541del (p.Gln846_Lys847del) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 26, 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:: RCV001857813.4

Allele description [Variation Report for NM_000251.3(MSH2):c.2536_2541del (p.Gln846_Lys847del)]

NM_000251.3(MSH2):c.2536_2541del (p.Gln846_Lys847del)

Gene:

MSH2:mutS homolog 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.2536_2541del (p.Gln846_Lys847del)

HGVS:

NC_000002.12:g.47480773_47480778del
NG_007110.2:g.82650_82655del
NM_000251.3:c.2536_2541delMANE SELECT
NM_001258281.1:c.2338_2343del
NP_000242.1:p.Gln846_Lys847del
NP_001245210.1:p.Gln780_Lys781del
LRG_218:g.82650_82655del
NC_000002.11:g.47707909_47707914del
NC_000002.11:g.47707912_47707917del
NM_000251.2:c.2536_2541delCAGAAA

Links:

dbSNP: rs879254133

NCBI 1000 Genomes Browser:

rs879254133

Molecular consequence:

NM_000251.3:c.2536_2541del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001258281.1:c.2338_2343del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

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

Recent activity

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Homo sapiens major histocompatibility complex, class I, A (HLA-A), mRNA
Homo sapiens major histocompatibility complex, class I, A (HLA-A), mRNA
gi|18034687|ref|NM_002116.2|

Nucleotide
Pathogen: environmental/food/other sample from Wohlfahrtiimonas chitiniclastica
Pathogen: environmental/food/other sample from Wohlfahrtiimonas chitiniclastica

biosample
Microbe sample from Wohlfahrtiimonas chitiniclastica
Microbe sample from Wohlfahrtiimonas chitiniclastica

biosample
NA45072
NA45072

biosample
Ihlea punctata voucher D24-Ipun-B-1 small subunit ribosomal RNA gene, partial se...
Ihlea punctata voucher D24-Ipun-B-1 small subunit ribosomal RNA gene, partial sequence
gi|2496045480|gb|OQ863571.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002143064	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 26, 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

SCV002143064

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 26, 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, SCV002143064.3

#	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.2536_2541del, results in the deletion of 2 amino acid(s) of the MSH2 protein (p.Gln846_Lys847del), 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 MSH2-related conditions. ClinVar contains an entry for this variant (Variation ID: 246167). 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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