NM_000249.4(MLH1):c.31del (p.Leu11fs) AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 7, 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:: RCV003451133.1

Allele description [Variation Report for NM_000249.4(MLH1):c.31del (p.Leu11fs)]

NM_000249.4(MLH1):c.31del (p.Leu11fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.31del (p.Leu11fs)

HGVS:

NC_000003.12:g.36993578del
NG_007109.2:g.5229del
NG_008418.1:g.4727del
NM_000249.4:c.31delMANE SELECT
NM_001167617.3:c.-486del
NM_001167618.3:c.-915del
NM_001167619.3:c.-828del
NM_001258271.2:c.31del
NM_001258273.2:c.-602del
NM_001258274.3:c.-1065del
NM_001354615.2:c.-596del
NM_001354616.2:c.-596del
NM_001354617.2:c.-688del
NM_001354618.2:c.-920del
NM_001354619.2:c.-1044del
NM_001354620.2:c.-254del
NM_001354621.2:c.-1013del
NM_001354622.2:c.-1126del
NM_001354623.2:c.-1035del
NM_001354624.2:c.-796del
NM_001354625.2:c.-694del
NM_001354626.2:c.-791del
NM_001354627.2:c.-1023del
NM_001354628.2:c.31del
NM_001354629.2:c.31del
NM_001354630.2:c.31del
NP_000240.1:p.Leu11fs
NP_001245200.1:p.Leu11fs
NP_001341557.1:p.Leu11fs
NP_001341558.1:p.Leu11fs
NP_001341559.1:p.Leu11fs
LRG_216:g.5229del
NC_000003.11:g.37035069del
NM_000249.3:c.31delC

Protein change:

L11fs

Links:

dbSNP: rs63749816

NCBI 1000 Genomes Browser:

rs63749816

Molecular consequence:

NM_001167617.3:c.-486del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-915del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-828del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-602del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-1065del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-596del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-596del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-688del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-920del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-1044del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-254del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-1013del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-1126del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-1035del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-796del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-694del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-791del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-1023del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.31del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258271.2:c.31del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354628.2:c.31del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354629.2:c.31del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354630.2:c.31del - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004186496	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Jul 7, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004186496

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Jul 7, 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., SCV004186496.1

#	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 7, 2024

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