NM_000249.4(MLH1):c.673_676del (p.Ser225fs) AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 17, 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:: RCV003452757.1

Allele description [Variation Report for NM_000249.4(MLH1):c.673_676del (p.Ser225fs)]

NM_000249.4(MLH1):c.673_676del (p.Ser225fs)

Gene:

MLH1:mutL homolog 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.673_676del (p.Ser225fs)

HGVS:

NC_000003.12:g.37012095_37012098del
NG_007109.2:g.23746_23749del
NM_000249.4:c.673_676delMANE SELECT
NM_001167617.3:c.379_382del
NM_001167618.3:c.-51_-48del
NM_001167619.3:c.-51_-48del
NM_001258271.2:c.673_676del
NM_001258273.2:c.-51_-48del
NM_001258274.3:c.-51_-48del
NM_001354615.2:c.-51_-48del
NM_001354616.2:c.-51_-48del
NM_001354617.2:c.-51_-48del
NM_001354618.2:c.-51_-48del
NM_001354619.2:c.-51_-48del
NM_001354620.2:c.379_382del
NM_001354621.2:c.-144_-141del
NM_001354622.2:c.-257_-254del
NM_001354623.2:c.-257_-254del
NM_001354624.2:c.-154_-151del
NM_001354625.2:c.-154_-151del
NM_001354626.2:c.-154_-151del
NM_001354627.2:c.-154_-151del
NM_001354628.2:c.673_676del
NM_001354629.2:c.574_577del
NM_001354630.2:c.673_676del
NP_000240.1:p.Ser225fs
NP_001161089.1:p.Ser127fs
NP_001245200.1:p.Ser225fs
NP_001341549.1:p.Ser127fs
NP_001341557.1:p.Ser225fs
NP_001341558.1:p.Ser192fs
NP_001341559.1:p.Ser225fs
LRG_216:g.23746_23749del
NC_000003.11:g.37053586_37053589del
NM_000249.3:c.673_676delAGTC
NM_000249.4:c.673_676del

Protein change:

S127fs

Links:

dbSNP: rs267607774

NCBI 1000 Genomes Browser:

rs267607774

Molecular consequence:

NM_001167618.3:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-51_-48del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-144_-141del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-257_-254del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-257_-254del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-154_-151del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-154_-151del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-154_-151del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-154_-151del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.673_676del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001167617.3:c.379_382del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258271.2:c.673_676del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354620.2:c.379_382del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354628.2:c.673_676del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354629.2:c.574_577del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354630.2:c.673_676del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Colorectal cancer, hereditary nonpolyposis, type 2 (LYNCH2)
Synonyms:: COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 2; Lynch syndrome II; MLH1-Related Lynch Syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012249; MedGen: C1333991; Orphanet: 144; OMIM: 609310

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BioProject
Sequence 42 from Patent WO2012170782
Sequence 42 from Patent WO2012170782
gi|583765361|emb|JC258752.1||pat|WO 170782|42

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004189881	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Jul 17, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004189881

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Jul 17, 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., SCV004189881.1

#	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: Sep 29, 2024

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