NM_000249.4(MLH1):c.8del (p.Phe3fs) 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:: RCV003450550.1

Allele description [Variation Report for NM_000249.4(MLH1):c.8del (p.Phe3fs)]

NM_000249.4(MLH1):c.8del (p.Phe3fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.8del (p.Phe3fs)

HGVS:

NC_000003.12:g.36993555del
NG_007109.2:g.5206del
NG_008418.1:g.4751del
NG_099042.2:g.84del
NM_000249.4:c.8delMANE SELECT
NM_001167617.3:c.-509del
NM_001167618.3:c.-938del
NM_001167619.3:c.-851del
NM_001258271.2:c.8del
NM_001258273.2:c.-625del
NM_001258274.3:c.-1088del
NM_001354615.2:c.-619del
NM_001354616.2:c.-619del
NM_001354617.2:c.-711del
NM_001354618.2:c.-943del
NM_001354619.2:c.-1067del
NM_001354620.2:c.-277del
NM_001354621.2:c.-1036del
NM_001354622.2:c.-1149del
NM_001354623.2:c.-1058del
NM_001354624.2:c.-819del
NM_001354625.2:c.-717del
NM_001354626.2:c.-814del
NM_001354627.2:c.-1046del
NM_001354628.2:c.8del
NM_001354629.2:c.8del
NM_001354630.2:c.8del
NP_000240.1:p.Phe3Serfs
NP_000240.1:p.Phe3fs
NP_001245200.1:p.Phe3fs
NP_001341557.1:p.Phe3fs
NP_001341558.1:p.Phe3fs
NP_001341559.1:p.Phe3fs
LRG_216t1:c.8del
LRG_216:g.5206del
LRG_216p1:p.Phe3Serfs
NC_000003.11:g.37035046del
NM_000249.3:c.8delT

Protein change:

F3fs

Molecular consequence:

NM_001167617.3:c.-509del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-938del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-851del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-625del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-1088del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-619del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-619del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-711del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-943del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-1067del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-277del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-1036del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-1149del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-1058del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-819del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-717del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-814del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-1046del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.8del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258271.2:c.8del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354628.2:c.8del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354629.2:c.8del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354630.2:c.8del - 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
SCV004189652	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

SCV004189652

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., SCV004189652.1

#	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: Dec 30, 2023

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