NM_000249.4(MLH1):c.170del (p.Lys57fs) AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 11, 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:: RCV003454277.1

Allele description [Variation Report for NM_000249.4(MLH1):c.170del (p.Lys57fs)]

NM_000249.4(MLH1):c.170del (p.Lys57fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.170del (p.Lys57fs)

HGVS:

NC_000003.12:g.36996672del
NG_007109.2:g.8323del
NG_008418.1:g.1634del
NM_000249.4:c.170delMANE SELECT
NM_001167617.3:c.-120del
NM_001167618.3:c.-554del
NM_001167619.3:c.-462del
NM_001258271.2:c.170del
NM_001258273.2:c.-517+3009del
NM_001258274.3:c.-699del
NM_001354615.2:c.-457del
NM_001354616.2:c.-462del
NM_001354617.2:c.-554del
NM_001354618.2:c.-554del
NM_001354619.2:c.-554del
NM_001354620.2:c.-120del
NM_001354621.2:c.-647del
NM_001354622.2:c.-760del
NM_001354623.2:c.-723+2782del
NM_001354624.2:c.-657del
NM_001354625.2:c.-560del
NM_001354626.2:c.-657del
NM_001354627.2:c.-657del
NM_001354628.2:c.170del
NM_001354629.2:c.170del
NM_001354630.2:c.170del
NP_000240.1:p.Lys57Serfs
NP_000240.1:p.Lys57fs
NP_001245200.1:p.Lys57fs
NP_001341557.1:p.Lys57fs
NP_001341558.1:p.Lys57fs
NP_001341559.1:p.Lys57fs
LRG_216t1:c.170del
LRG_216:g.8323del
LRG_216p1:p.Lys57Serfs
NC_000003.11:g.37038163del
NM_000249.3:c.170delA

Protein change:

K57fs

Molecular consequence:

NM_001167617.3:c.-120del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-554del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-462del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-699del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-457del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-462del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-554del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-554del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-554del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-120del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-647del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-760del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-657del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-560del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-657del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-657del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.170del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258271.2:c.170del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354628.2:c.170del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354629.2:c.170del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354630.2:c.170del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258273.2:c.-517+3009del - intron variant - [Sequence Ontology: SO:0001627]
NM_001354623.2:c.-723+2782del - intron variant - [Sequence Ontology: SO:0001627]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004189778	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Jul 11, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004189778

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Jul 11, 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., SCV004189778.1

#	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: May 1, 2024

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