NM_000249.4(MLH1):c.1896+1del AND Lynch syndrome

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

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000075406.3

Allele description [Variation Report for NM_000249.4(MLH1):c.1896+1del]

NM_000249.4(MLH1):c.1896+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.1896+1del
HGVS:
  • NC_000003.12:g.37047684del
  • NG_007109.2:g.59335del
  • NM_000249.4:c.1896+1delMANE SELECT
  • NM_001167617.3:c.1602+1del
  • NM_001167618.3:c.1173+1del
  • NM_001167619.3:c.1173+1del
  • NM_001258271.2:c.1896+1del
  • NM_001258273.2:c.1173+1del
  • NM_001258274.3:c.1173+1del
  • NM_001354615.2:c.1173+1del
  • NM_001354616.2:c.1173+1del
  • NM_001354617.2:c.1173+1del
  • NM_001354618.2:c.1173+1del
  • NM_001354619.2:c.1173+1del
  • NM_001354620.2:c.1602+1del
  • NM_001354621.2:c.873+1del
  • NM_001354622.2:c.873+1del
  • NM_001354623.2:c.873+1del
  • NM_001354624.2:c.822+1del
  • NM_001354625.2:c.822+1del
  • NM_001354626.2:c.822+1del
  • NM_001354627.2:c.822+1del
  • NM_001354628.2:c.1896+1del
  • NM_001354629.2:c.1797+1del
  • NM_001354630.2:c.1732-833del
  • LRG_216t1:c.1896+1del
  • LRG_216:g.59335del
  • NC_000003.11:g.37089175del
  • NM_000249.3:c.1896+1delG
Links:
dbSNP: rs267607868
NCBI 1000 Genomes Browser:
rs267607868
Molecular consequence:
  • NM_001354630.2:c.1732-833del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.4:c.1896+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167617.3:c.1602+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167618.3:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167619.3:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258271.2:c.1896+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258273.2:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258274.3:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354615.2:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354616.2:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354617.2:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354618.2:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354619.2:c.1173+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354620.2:c.1602+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354621.2:c.873+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354622.2:c.873+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354623.2:c.873+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354624.2:c.822+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354625.2:c.822+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354626.2:c.822+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354627.2:c.822+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354628.2:c.1896+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354629.2:c.1797+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Lynch syndrome
Synonyms:
Familial nonpolyposis colon cancer
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100; OMIM: PS120435

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000106399International Society for Gastrointestinal Hereditary Tumours (InSiGHT)reviewed by expert panel
Likely pathogenic
(Jun 21, 2019)
germlinecuration

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedcuration

Details of each submission

From International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000106399.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

Interrupts canonical donor splice site

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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