NM_000249.4(MLH1):c.589-1G>A AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 11, 2022
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:: RCV002497722.1

Allele description [Variation Report for NM_000249.4(MLH1):c.589-1G>A]

NM_000249.4(MLH1):c.589-1G>A

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.589-1G>A

HGVS:

NC_000003.12:g.37012010G>A
NG_007109.2:g.23661G>A
NM_000249.4:c.589-1G>AMANE SELECT
NM_001167617.3:c.295-1G>A
NM_001167618.3:c.-135-1G>A
NM_001167619.3:c.-135-1G>A
NM_001258271.2:c.589-1G>A
NM_001258273.2:c.-135-1G>A
NM_001258274.3:c.-135-1G>A
NM_001354615.2:c.-135-1G>A
NM_001354616.2:c.-135-1G>A
NM_001354617.2:c.-135-1G>A
NM_001354618.2:c.-135-1G>A
NM_001354619.2:c.-135-1G>A
NM_001354620.2:c.295-1G>A
NM_001354621.2:c.-228-1G>A
NM_001354622.2:c.-341-1G>A
NM_001354623.2:c.-341-1G>A
NM_001354624.2:c.-238-1G>A
NM_001354625.2:c.-238-1G>A
NM_001354626.2:c.-238-1G>A
NM_001354627.2:c.-238-1G>A
NM_001354628.2:c.589-1G>A
NM_001354629.2:c.490-1G>A
NM_001354630.2:c.589-1G>A
LRG_216t1:c.589-1G>A
LRG_216:g.23661G>A
NC_000003.11:g.37053501G>A
NM_000249.3:c.589-1G>A

Links:

dbSNP: rs587779027

NCBI 1000 Genomes Browser:

rs587779027

Molecular consequence:

NM_000249.4:c.589-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001167617.3:c.295-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001167618.3:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001167619.3:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001258271.2:c.589-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001258273.2:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001258274.3:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354615.2:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354616.2:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354617.2:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354618.2:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354619.2:c.-135-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354620.2:c.295-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354621.2:c.-228-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354622.2:c.-341-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354623.2:c.-341-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354624.2:c.-238-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354625.2:c.-238-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354626.2:c.-238-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354627.2:c.-238-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354628.2:c.589-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354629.2:c.490-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354630.2:c.589-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Mismatch repair cancer syndrome 1 (MMRCS1)
Synonyms:: BRAIN TUMOR-POLYPOSIS SYNDROME 1; BTP1 SYNDROME; CHILDHOOD CANCER SYNDROME; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010159; MedGen: C5399763; Orphanet: 252202; OMIM: 276300

Name:: Muir-Torré syndrome (MRTES)
Synonyms:: Muir-Torre syndrome; Cutaneous sebaceous neoplasms and keratoacanthomas multiple with gastrointestinal and other carcinomas; MSH2-Related Muir-Torre Syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008018; MedGen: C1321489; Orphanet: 587; OMIM: 158320

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
SCV002811136	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 11, 2022)	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

SCV002811136

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 11, 2022)

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

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 Fulgent Genetics, Fulgent Genetics, SCV002811136.1

#	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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