NM_000251.3(MSH2):c.2658G>A (p.Glu886=) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Likely benign (1 submission)
Last evaluated:: Dec 15, 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:: RCV003595494.2

Allele description [Variation Report for NM_000251.3(MSH2):c.2658G>A (p.Glu886=)]

NM_000251.3(MSH2):c.2658G>A (p.Glu886=)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.2658G>A (p.Glu886=)

HGVS:

NC_000002.12:g.47482802G>A
NG_007110.2:g.84679G>A
NM_000251.3:c.2658G>AMANE SELECT
NM_001258281.1:c.2460G>A
NM_001406631.1:c.2634+1931G>A
NM_001406632.1:c.2634+1931G>A
NM_001406633.1:c.2634+1931G>A
NM_001406634.1:c.2634+1931G>A
NM_001406635.1:c.2634+1931G>A
NM_001406636.1:c.2601+1931G>A
NM_001406637.1:c.2634+1931G>A
NM_001406638.1:c.2697G>A
NM_001406639.1:c.2634+1931G>A
NM_001406640.1:c.2634+1931G>A
NM_001406641.1:c.2658G>A
NM_001406642.1:c.2634+1931G>A
NM_001406643.1:c.2634+1931G>A
NM_001406644.1:c.2634+1931G>A
NM_001406645.1:c.2634+1931G>A
NM_001406646.1:c.2634+1931G>A
NM_001406647.1:c.2484+1931G>A
NM_001406649.1:c.2508G>A
NM_001406650.1:c.2508G>A
NM_001406651.1:c.2484+1931G>A
NM_001406652.1:c.2484+1931G>A
NM_001406654.1:c.2214+1931G>A
NM_001406656.1:c.1737+1931G>A
NM_001406658.1:c.1302G>A
NM_001406659.1:c.1302G>A
NM_001406660.1:c.1302G>A
NM_001406661.1:c.1302G>A
NM_001406662.1:c.1302G>A
NM_001406669.1:c.1278+1931G>A
NM_001406674.1:c.2634+1931G>A
NP_000242.1:p.Glu886=
NP_000242.1:p.Glu886=
NP_001245210.1:p.Glu820=
NP_001393567.1:p.Glu899=
NP_001393570.1:p.Glu886=
NP_001393578.1:p.Glu836=
NP_001393579.1:p.Glu836=
NP_001393587.1:p.Glu434=
NP_001393588.1:p.Glu434=
NP_001393589.1:p.Glu434=
NP_001393590.1:p.Glu434=
NP_001393591.1:p.Glu434=
LRG_218t1:c.2658G>A
LRG_218:g.84679G>A
LRG_218p1:p.Glu886=
NC_000002.11:g.47709941G>A
NM_000251.2:c.2658G>A
NR_176235.1:n.2694G>A
NR_176237.1:n.2694G>A
NR_176239.1:n.2694G>A
NR_176242.1:n.2694G>A
NR_176250.1:n.2434G>A

Molecular consequence:

NM_001406631.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406632.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406633.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406634.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406635.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406636.1:c.2601+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406637.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406639.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406640.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406642.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406643.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406644.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406645.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406646.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406647.1:c.2484+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406651.1:c.2484+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406652.1:c.2484+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406654.1:c.2214+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406656.1:c.1737+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406669.1:c.1278+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406674.1:c.2634+1931G>A - intron variant - [Sequence Ontology: SO:0001627]
NR_176235.1:n.2694G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176237.1:n.2694G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176239.1:n.2694G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176242.1:n.2694G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176250.1:n.2434G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000251.3:c.2658G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001258281.1:c.2460G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406638.1:c.2697G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406641.1:c.2658G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406649.1:c.2508G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406650.1:c.2508G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406658.1:c.1302G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406659.1:c.1302G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406660.1:c.1302G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406661.1:c.1302G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406662.1:c.1302G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

Recent activity

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calpain-3 isoform X6 [Macaca fascicularis]
calpain-3 isoform X6 [Macaca fascicularis]
gi|982256489|ref|XP_015307943.1|

Protein
PREDICTED: Homo sapiens hippocalcin (HPCA), transcript variant X3, mRNA
PREDICTED: Homo sapiens hippocalcin (HPCA), transcript variant X3, mRNA
gi|2462508405|ref|XM_054336226.1|

Nucleotide
Pathogen: clinical or host-associated sample from Escherichia coli
Pathogen: clinical or host-associated sample from Escherichia coli

biosample
PREDICTED: Momordica charantia transcriptional regulator SUPERMAN-like (LOC11102...
PREDICTED: Momordica charantia transcriptional regulator SUPERMAN-like (LOC111025958), mRNA
gi|1229757009|ref|XM_022303895.1|

Nucleotide
dihydroxyacetone kinase, DhaK subunit [Propionibacterium sp. KPL2005]
dihydroxyacetone kinase, DhaK subunit [Propionibacterium sp. KPL2005]
gi|550724779|gb|ERS24607.1||gnl|WGS |HMPREF1301_00598T0

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004285964	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 15, 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

SCV004285964

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 15, 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, SCV004285964.1

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

#	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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