NM_000251.3(MSH2):c.2520_2521del (p.Ile841fs) AND Lynch syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 9, 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:: RCV003455478.1

Allele description [Variation Report for NM_000251.3(MSH2):c.2520_2521del (p.Ile841fs)]

NM_000251.3(MSH2):c.2520_2521del (p.Ile841fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.2520_2521del (p.Ile841fs)

HGVS:

NC_000002.12:g.47480757_47480758del
NG_007110.2:g.82634_82635del
NM_000251.3:c.2520_2521delMANE SELECT
NM_001258281.1:c.2322_2323del
NM_001406631.1:c.2520_2521delAA
NM_001406632.1:c.2520_2521delAA
NM_001406633.1:c.2520_2521delAA
NM_001406634.1:c.2520_2521delAA
NM_001406635.1:c.2520_2521delAA
NM_001406636.1:c.2487_2488delAA
NM_001406637.1:c.2520_2521delAA
NM_001406638.1:c.2559_2560delAA
NM_001406639.1:c.2520_2521delAA
NM_001406640.1:c.2520_2521delAA
NM_001406641.1:c.2520_2521delAA
NM_001406642.1:c.2520_2521delAA
NM_001406643.1:c.2520_2521delAA
NM_001406644.1:c.2520_2521delAA
NM_001406645.1:c.2520_2521delAA
NM_001406646.1:c.2520_2521delAA
NM_001406647.1:c.2370_2371delAA
NM_001406648.1:c.2520_2521delAA
NM_001406649.1:c.2370_2371delAA
NM_001406650.1:c.2370_2371delAA
NM_001406651.1:c.2370_2371delAA
NM_001406652.1:c.2370_2371delAA
NM_001406653.1:c.2460_2461delAA
NM_001406654.1:c.2100_2101delAA
NM_001406656.1:c.1623_1624delAA
NM_001406658.1:c.1164_1165delAA
NM_001406659.1:c.1164_1165delAA
NM_001406660.1:c.1164_1165delAA
NM_001406661.1:c.1164_1165delAA
NM_001406662.1:c.1164_1165delAA
NM_001406669.1:c.1164_1165delAA
NM_001406674.1:c.2520_2521delAA
NP_000242.1:p.Ile841Argfs
NP_000242.1:p.Ile841fs
NP_001245210.1:p.Ile775fs
NP_001393560.1:p.Ile841Argfs
NP_001393561.1:p.Ile841Argfs
NP_001393562.1:p.Ile841Argfs
NP_001393563.1:p.Ile841Argfs
NP_001393564.1:p.Ile841Argfs
NP_001393565.1:p.Ile830Argfs
NP_001393566.1:p.Ile841Argfs
NP_001393567.1:p.Ile854Argfs
NP_001393568.1:p.Ile841Argfs
NP_001393569.1:p.Ile841Argfs
NP_001393570.1:p.Ile841Argfs
NP_001393571.1:p.Ile841Argfs
NP_001393572.1:p.Ile841Argfs
NP_001393573.1:p.Ile841Argfs
NP_001393574.1:p.Ile841Argfs
NP_001393575.1:p.Ile841Argfs
NP_001393576.1:p.Ile791Argfs
NP_001393577.1:p.Ile841Argfs
NP_001393578.1:p.Ile791Argfs
NP_001393579.1:p.Ile791Argfs
NP_001393580.1:p.Ile791Argfs
NP_001393581.1:p.Ile791Argfs
NP_001393582.1:p.Ile821Argfs
NP_001393583.1:p.Ile701Argfs
NP_001393585.1:p.Ile542Argfs
NP_001393587.1:p.Ile389Argfs
NP_001393588.1:p.Ile389Argfs
NP_001393589.1:p.Ile389Argfs
NP_001393590.1:p.Ile389Argfs
NP_001393591.1:p.Ile389Argfs
NP_001393598.1:p.Ile389Argfs
NP_001393603.1:p.Ile841Argfs
LRG_218t1:c.2520_2521del
LRG_218:g.82634_82635del
LRG_218p1:p.Ile841Argfs
NC_000002.11:g.47707896_47707897del
NM_000251.1:c.2520_2521delAA
NM_000251.2:c.2520_2521delAA
NR_176230.1:n.2556_2557delAA
NR_176231.1:n.2524_2525delAA
NR_176232.1:n.2556_2557delAA
NR_176233.1:n.2398_2399delAA
NR_176234.1:n.2556_2557delAA
NR_176235.1:n.2556_2557delAA
NR_176236.1:n.2556_2557delAA
NR_176237.1:n.2556_2557delAA
NR_176238.1:n.2689_2690delAA
NR_176239.1:n.2556_2557delAA
NR_176240.1:n.2351_2352delAA
NR_176241.1:n.2556_2557delAA
NR_176242.1:n.2556_2557delAA
NR_176243.1:n.2406_2407delAA
NR_176244.1:n.2556_2557delAA
NR_176245.1:n.2556_2557delAA
NR_176246.1:n.2556_2557delAA
NR_176247.1:n.2556_2557delAA
NR_176248.1:n.2556_2557delAA
NR_176249.1:n.2786_2787delAA
NR_176250.1:n.2296_2297delAA

Protein change:

I775fs

Molecular consequence:

NM_000251.3:c.2520_2521del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258281.1:c.2322_2323del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406631.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406632.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406633.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406634.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406635.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406636.1:c.2487_2488delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406637.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406638.1:c.2559_2560delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406639.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406640.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406641.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406642.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406643.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406644.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406645.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406646.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406647.1:c.2370_2371delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406648.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406649.1:c.2370_2371delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406650.1:c.2370_2371delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406651.1:c.2370_2371delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406652.1:c.2370_2371delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406653.1:c.2460_2461delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406654.1:c.2100_2101delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406656.1:c.1623_1624delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406658.1:c.1164_1165delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406659.1:c.1164_1165delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406660.1:c.1164_1165delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406661.1:c.1164_1165delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406662.1:c.1164_1165delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406669.1:c.1164_1165delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406674.1:c.2520_2521delAA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Lynch syndrome 1
Synonyms:: COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 1; MSH2-Related Hereditary Non-Polyposis Colon Cancer; Lynch syndrome I; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007356; MedGen: C2936783; Orphanet: 144; OMIM: 120435

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
SCV004187905	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Aug 9, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004187905

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Aug 9, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV004187905.1

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

Description

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

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

Last Updated: Jun 9, 2024

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