NM_000249.4(MLH1):c.588+1del AND Lynch syndrome II

Clinical significance:Likely pathogenic (Last evaluated: Nov 21, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001253171.1

Allele description [Variation Report for NM_000249.4(MLH1):c.588+1del]

NM_000249.4(MLH1):c.588+1del

Gene:
MLH1:mutL homolog 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3p22.2
Genomic location:
Preferred name:
NM_000249.4(MLH1):c.588+1del
HGVS:
  • NC_000003.12:g.37011863del
  • NG_007109.2:g.23514del
  • NM_000249.3:c.588+1delG
  • NM_000249.4:c.588+1delMANE SELECT
  • NM_001167617.3:c.294+1del
  • NM_001167618.3:c.-136+1del
  • NM_001167619.3:c.-136+1del
  • NM_001258271.2:c.588+1del
  • NM_001258273.2:c.-136+1del
  • NM_001258274.3:c.-136+1del
  • NM_001354615.2:c.-136+1del
  • NM_001354616.2:c.-136+1del
  • NM_001354617.2:c.-136+1del
  • NM_001354618.2:c.-136+1del
  • NM_001354619.2:c.-136+1del
  • NM_001354620.2:c.294+1del
  • NM_001354621.2:c.-229+1del
  • NM_001354622.2:c.-342+1del
  • NM_001354623.2:c.-342+1del
  • NM_001354624.2:c.-239+1del
  • NM_001354625.2:c.-239+1del
  • NM_001354626.2:c.-239+1del
  • NM_001354627.2:c.-239+1del
  • NM_001354628.2:c.588+1del
  • NM_001354629.2:c.489+1del
  • NM_001354630.2:c.588+1del
  • LRG_216t1:c.588+1del
  • LRG_216:g.23514del
  • NC_000003.11:g.37053354del
Links:
dbSNP: rs267607773
NCBI 1000 Genomes Browser:
rs267607773
Molecular consequence:
  • NM_000249.3:c.588+1delG - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_000249.4:c.588+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167617.3:c.294+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167618.3:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167619.3:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258271.2:c.588+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258273.2:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258274.3:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354615.2:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354616.2:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354617.2:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354618.2:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354619.2:c.-136+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354620.2:c.294+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354621.2:c.-229+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354622.2:c.-342+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354623.2:c.-342+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354624.2:c.-239+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354625.2:c.-239+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354626.2:c.-239+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354627.2:c.-239+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354628.2:c.588+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354629.2:c.489+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354630.2:c.588+1del - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
1

Condition(s)

Name:
Lynch syndrome II (HNPCC2)
Synonyms:
COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 2; MLH1-Related Hereditary Non-Polyposis Colon Cancer; MLH1-Related Lynch Syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012249; MedGen: C1333991; Orphanet: 144; OMIM: 609310

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001428751Institute of Human Genetics, University of Leipzig Medical Centercriteria provided, single submitter
Likely pathogenic
(Nov 21, 2019)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical 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 Institute of Human Genetics, University of Leipzig Medical Center, SCV001428751.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 25, 2021

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