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NM_000249.4(MLH1):c.116+1G>T AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 3, 2019
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:
RCV002376988.2

Allele description [Variation Report for NM_000249.4(MLH1):c.116+1G>T]

NM_000249.4(MLH1):c.116+1G>T

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.116+1G>T
HGVS:
  • NC_000003.12:g.36993664G>T
  • NG_007109.2:g.5315G>T
  • NG_008418.1:g.4641C>A
  • NG_099042.1:g.57G>T
  • NG_099042.2:g.193G>T
  • NM_000249.4:c.116+1G>TMANE SELECT
  • NM_001167617.3:c.-400G>T
  • NM_001167618.3:c.-829G>T
  • NM_001167619.3:c.-742G>T
  • NM_001258271.2:c.116+1G>T
  • NM_001258273.2:c.-517+1G>T
  • NM_001258274.3:c.-979G>T
  • NM_001354615.2:c.-511+1G>T
  • NM_001354616.2:c.-511+1G>T
  • NM_001354617.2:c.-603+1G>T
  • NM_001354618.2:c.-834G>T
  • NM_001354619.2:c.-958G>T
  • NM_001354620.2:c.-169+1G>T
  • NM_001354621.2:c.-927G>T
  • NM_001354622.2:c.-1040G>T
  • NM_001354623.2:c.-949G>T
  • NM_001354624.2:c.-711+1G>T
  • NM_001354625.2:c.-609+1G>T
  • NM_001354626.2:c.-706+1G>T
  • NM_001354627.2:c.-937G>T
  • NM_001354628.2:c.116+1G>T
  • NM_001354629.2:c.116+1G>T
  • NM_001354630.2:c.116+1G>T
  • LRG_216t1:c.116+1G>T
  • LRG_216:g.5315G>T
  • NC_000003.11:g.37035155G>T
  • NM_000249.3:c.116+1G>T
Links:
dbSNP: rs267607709
NCBI 1000 Genomes Browser:
rs267607709
Molecular consequence:
  • NM_001167617.3:c.-400G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-829G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-742G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-979G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-834G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-958G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-927G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-1040G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354623.2:c.-949G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-937G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000249.4:c.116+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258271.2:c.116+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258273.2:c.-517+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354615.2:c.-511+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354616.2:c.-511+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354617.2:c.-603+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354620.2:c.-169+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354624.2:c.-711+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354625.2:c.-609+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354626.2:c.-706+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354628.2:c.116+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354629.2:c.116+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354630.2:c.116+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002624029Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(May 3, 2019) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002624029.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.116+1G>T intronic variant results from a G to T substitution one nucleotide after coding exon 1 of the MLH1 gene. This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice donor site; however, direct evidence is unavailable. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

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

Last Updated: Sep 29, 2024