NM_000251.3(MSH2):c.897T>A (p.Tyr299Ter) AND Lynch syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 28, 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:: RCV003455811.1

Allele description [Variation Report for NM_000251.3(MSH2):c.897T>A (p.Tyr299Ter)]

NM_000251.3(MSH2):c.897T>A (p.Tyr299Ter)

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.897T>A (p.Tyr299Ter)

HGVS:

NC_000002.12:g.47414373T>A
NG_007110.2:g.16250T>A
NM_000251.3:c.897T>AMANE SELECT
NM_001258281.1:c.699T>A
NM_001406631.1:c.897T>A
NM_001406632.1:c.897T>A
NM_001406633.1:c.897T>A
NM_001406634.1:c.897T>A
NM_001406635.1:c.897T>A
NM_001406636.1:c.864T>A
NM_001406637.1:c.897T>A
NM_001406638.1:c.897T>A
NM_001406639.1:c.897T>A
NM_001406640.1:c.897T>A
NM_001406641.1:c.897T>A
NM_001406642.1:c.897T>A
NM_001406643.1:c.897T>A
NM_001406644.1:c.897T>A
NM_001406645.1:c.897T>A
NM_001406646.1:c.897T>A
NM_001406647.1:c.792+1813T>A
NM_001406648.1:c.897T>A
NM_001406649.1:c.792+1813T>A
NM_001406650.1:c.792+1813T>A
NM_001406651.1:c.792+1813T>A
NM_001406652.1:c.792+1813T>A
NM_001406653.1:c.837T>A
NM_001406654.1:c.477T>A
NM_001406655.1:c.897T>A
NM_001406656.1:c.-1T>A
NM_001406657.1:c.897T>A
NM_001406658.1:c.-527+1813T>A
NM_001406659.1:c.-572T>A
NM_001406660.1:c.-769T>A
NM_001406661.1:c.-724T>A
NM_001406662.1:c.-641T>A
NM_001406666.1:c.897T>A
NM_001406669.1:c.-572T>A
NM_001406672.1:c.792+1813T>A
NM_001406674.1:c.897T>A
NP_000242.1:p.Tyr299Ter
NP_000242.1:p.Tyr299Ter
NP_001245210.1:p.Tyr233Ter
NP_001393560.1:p.Tyr299Ter
NP_001393561.1:p.Tyr299Ter
NP_001393562.1:p.Tyr299Ter
NP_001393563.1:p.Tyr299Ter
NP_001393564.1:p.Tyr299Ter
NP_001393565.1:p.Tyr288Ter
NP_001393566.1:p.Tyr299Ter
NP_001393567.1:p.Tyr299Ter
NP_001393568.1:p.Tyr299Ter
NP_001393569.1:p.Tyr299Ter
NP_001393570.1:p.Tyr299Ter
NP_001393571.1:p.Tyr299Ter
NP_001393572.1:p.Tyr299Ter
NP_001393573.1:p.Tyr299Ter
NP_001393574.1:p.Tyr299Ter
NP_001393575.1:p.Tyr299Ter
NP_001393577.1:p.Tyr299Ter
NP_001393582.1:p.Tyr279Ter
NP_001393583.1:p.Tyr159Ter
NP_001393584.1:p.Tyr299Ter
NP_001393586.1:p.Tyr299Ter
NP_001393595.1:p.Tyr299Ter
NP_001393603.1:p.Tyr299Ter
LRG_218t1:c.897T>A
LRG_218:g.16250T>A
LRG_218p1:p.Tyr299Ter
NC_000002.11:g.47641512T>A
NM_000251.1:c.897T>A
NM_000251.2:c.897T>A
NR_176230.1:n.933T>A
NR_176231.1:n.933T>A
NR_176232.1:n.933T>A
NR_176234.1:n.933T>A
NR_176235.1:n.933T>A
NR_176236.1:n.933T>A
NR_176237.1:n.933T>A
NR_176238.1:n.933T>A
NR_176239.1:n.933T>A
NR_176240.1:n.933T>A
NR_176241.1:n.933T>A
NR_176242.1:n.933T>A
NR_176244.1:n.933T>A
NR_176245.1:n.933T>A
NR_176246.1:n.933T>A
NR_176247.1:n.933T>A
NR_176248.1:n.933T>A
NR_176249.1:n.933T>A

Protein change:

Y159*

Molecular consequence:

NM_001406656.1:c.-1T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406659.1:c.-572T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406660.1:c.-769T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406661.1:c.-724T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406662.1:c.-641T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406669.1:c.-572T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406647.1:c.792+1813T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406649.1:c.792+1813T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406650.1:c.792+1813T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406651.1:c.792+1813T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406652.1:c.792+1813T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406658.1:c.-527+1813T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406672.1:c.792+1813T>A - intron variant - [Sequence Ontology: SO:0001627]
NR_176230.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176231.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176232.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176234.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176235.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176236.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176237.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176238.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176239.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176240.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176241.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176242.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176244.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176245.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176246.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176247.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176248.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176249.1:n.933T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000251.3:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001258281.1:c.699T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406631.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406632.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406633.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406634.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406635.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406636.1:c.864T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406637.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406638.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406639.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406640.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406641.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406642.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406643.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406644.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406645.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406646.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406648.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406653.1:c.837T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406654.1:c.477T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406655.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406657.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406666.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001406674.1:c.897T>A - nonsense - [Sequence Ontology: SO:0001587]

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 TBC1 domain family member 23 (TBC1D23), transcript variant 1, mRNA
Homo sapiens TBC1 domain family member 23 (TBC1D23), transcript variant 1, mRNA
gi|1519245870|ref|NM_001199198.3|

Nucleotide
Melampsora larici-populina 98AG31
Melampsora larici-populina 98AG31
Melampsora larici-populina 98AG31 RefSeq Genome

BioProject
BioProject Links for Protein (Select 599364840) (1)
BioProject
hypothetical protein BD777DRAFT_129525 [Yarrowia lipolytica]
hypothetical protein BD777DRAFT_129525 [Yarrowia lipolytica]
gi|1498519676|gb|RMI95675.1||gnl|WG B|BD777DRAFT_129525

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004187862	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Jul 28, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004187862

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Jul 28, 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., SCV004187862.1

#	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 termination codon and is 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: Sep 29, 2024

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