NM_000249.4(MLH1):c.100_103del (p.Lys33_Glu34insTer) AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 10, 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:: RCV003452724.1

Allele description [Variation Report for NM_000249.4(MLH1):c.100_103del (p.Lys33_Glu34insTer)]

NM_000249.4(MLH1):c.100_103del (p.Lys33_Glu34insTer)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.100_103del (p.Lys33_Glu34insTer)

HGVS:

NC_000003.12:g.36993647_36993650del
NG_007109.2:g.5298_5301del
NG_008418.1:g.4656_4659del
NG_099042.1:g.40_43del
NG_099042.2:g.176_179del
NM_000249.4:c.100_103delMANE SELECT
NM_001167617.3:c.-417_-414del
NM_001167618.3:c.-846_-843del
NM_001167619.3:c.-759_-756del
NM_001258271.2:c.100_103del
NM_001258273.2:c.-533_-530del
NM_001258274.3:c.-996_-993del
NM_001354615.2:c.-527_-524del
NM_001354616.2:c.-527_-524del
NM_001354617.2:c.-619_-616del
NM_001354618.2:c.-851_-848del
NM_001354619.2:c.-975_-972del
NM_001354620.2:c.-185_-182del
NM_001354621.2:c.-944_-941del
NM_001354622.2:c.-1057_-1054del
NM_001354623.2:c.-966_-963del
NM_001354624.2:c.-727_-724del
NM_001354625.2:c.-625_-622del
NM_001354626.2:c.-722_-719del
NM_001354627.2:c.-954_-951del
NM_001354628.2:c.100_103del
NM_001354629.2:c.100_103del
NM_001354630.2:c.100_103del
NP_000240.1:p.Glu34Terfs
NP_000240.1:p.Lys33_Glu34insTer
NP_001245200.1:p.Lys33_Glu34insTer
NP_001341557.1:p.Lys33_Glu34insTer
NP_001341558.1:p.Lys33_Glu34insTer
NP_001341559.1:p.Lys33_Glu34insTer
LRG_216t1:c.100_103del
LRG_216:g.5298_5301del
LRG_216p1:p.Glu34Terfs
NC_000003.11:g.37035137_37035140del
NC_000003.11:g.37035138_37035141del
NM_000249.3:c.100_103delGAGA

Molecular consequence:

NM_001167617.3:c.-417_-414del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-846_-843del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-759_-756del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-533_-530del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-996_-993del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-527_-524del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-527_-524del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-619_-616del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-851_-848del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-975_-972del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-185_-182del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-944_-941del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-1057_-1054del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-966_-963del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-727_-724del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-625_-622del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-722_-719del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-954_-951del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.100_103del - nonsense - [Sequence Ontology: SO:0001587]
NM_001258271.2:c.100_103del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354628.2:c.100_103del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354629.2:c.100_103del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354630.2:c.100_103del - nonsense - [Sequence Ontology: SO:0001587]

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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Mus musculus mitochondrial ribosomal protein S17 (Mrps17), mRNA
Mus musculus mitochondrial ribosomal protein S17 (Mrps17), mRNA
gi|13384853|ref|NM_025450.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004186419	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Jul 10, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004186419

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Jul 10, 2023)

unknown

clinical testing

Citation Link

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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., SCV004186419.1

#	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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