NM_000249.4(MLH1):c.122A>T (p.Asp41Val) AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 24, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV003449521.2

Allele description [Variation Report for NM_000249.4(MLH1):c.122A>T (p.Asp41Val)]

NM_000249.4(MLH1):c.122A>T (p.Asp41Val)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.122A>T (p.Asp41Val)

HGVS:

NC_000003.12:g.36996624A>T
NG_007109.2:g.8275A>T
NG_008418.1:g.1681T>A
NM_000249.4:c.122A>TMANE SELECT
NM_001167617.3:c.-168A>T
NM_001167618.3:c.-602A>T
NM_001167619.3:c.-510A>T
NM_001258271.2:c.122A>T
NM_001258273.2:c.-517+2961A>T
NM_001258274.3:c.-747A>T
NM_001354615.2:c.-505A>T
NM_001354616.2:c.-510A>T
NM_001354617.2:c.-602A>T
NM_001354618.2:c.-602A>T
NM_001354619.2:c.-602A>T
NM_001354620.2:c.-168A>T
NM_001354621.2:c.-695A>T
NM_001354622.2:c.-808A>T
NM_001354623.2:c.-723+2734A>T
NM_001354624.2:c.-705A>T
NM_001354625.2:c.-608A>T
NM_001354626.2:c.-705A>T
NM_001354627.2:c.-705A>T
NM_001354628.2:c.122A>T
NM_001354629.2:c.122A>T
NM_001354630.2:c.122A>T
NP_000240.1:p.Asp41Val
NP_000240.1:p.Asp41Val
NP_001245200.1:p.Asp41Val
NP_001341557.1:p.Asp41Val
NP_001341558.1:p.Asp41Val
NP_001341559.1:p.Asp41Val
LRG_216t1:c.122A>T
LRG_216:g.8275A>T
LRG_216p1:p.Asp41Val
NC_000003.11:g.37038115A>T
NM_000249.3:c.122A>T

Protein change:

D41V

Links:

dbSNP: rs63751094

NCBI 1000 Genomes Browser:

rs63751094

Molecular consequence:

NM_001167617.3:c.-168A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-602A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-510A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-747A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-505A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-510A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-602A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-602A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-602A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-168A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-695A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-808A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-705A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-608A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-705A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-705A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-517+2961A>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001354623.2:c.-723+2734A>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000249.4:c.122A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.122A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.122A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.122A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.122A>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004185561	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Jul 18, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV005057951	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 24, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004185561

Myriad Genetics, Inc.

criteria provided, single submitter

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

Likely pathogenic
(Jul 18, 2023)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV005057951

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 24, 2024)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

Classification of genetic variants in genes associated with Lynch syndrome using a clinical history weighting algorithm.

Morris B, Hughes E, Rosenthal E, Gutin A, Bowles KR.

BMC Genet. 2016 Jul 1;17(1):99. doi: 10.1186/s12863-016-0407-0.

PubMed [citation]

PMID:: 27363726
PMCID:: PMC4929734

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Myriad Genetics, Inc., SCV004185561.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant is considered likely pathogenic. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 27363726].

#	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

From Baylor Genetics, SCV005057951.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	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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