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NM_000249.4(MLH1):c.2250C>G (p.Tyr750Ter) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 2, 2015
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:
RCV000482247.1

Allele description [Variation Report for NM_000249.4(MLH1):c.2250C>G (p.Tyr750Ter)]

NM_000249.4(MLH1):c.2250C>G (p.Tyr750Ter)

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.2250C>G (p.Tyr750Ter)
HGVS:
  • NC_000003.12:g.37050632C>G
  • NG_007109.2:g.62283C>G
  • NG_053016.1:g.131186G>C
  • NM_000249.4:c.2250C>GMANE SELECT
  • NM_001167617.3:c.1956C>G
  • NM_001167618.3:c.1527C>G
  • NM_001167619.3:c.1527C>G
  • NM_001258271.2:c.2043C>G
  • NM_001258273.2:c.1527C>G
  • NM_001258274.3:c.1527C>G
  • NM_001354615.2:c.1527C>G
  • NM_001354616.2:c.1527C>G
  • NM_001354617.2:c.1527C>G
  • NM_001354618.2:c.1527C>G
  • NM_001354619.2:c.1527C>G
  • NM_001354620.2:c.1956C>G
  • NM_001354621.2:c.1227C>G
  • NM_001354622.2:c.1227C>G
  • NM_001354623.2:c.1227C>G
  • NM_001354624.2:c.1176C>G
  • NM_001354625.2:c.1176C>G
  • NM_001354626.2:c.1176C>G
  • NM_001354627.2:c.1176C>G
  • NM_001354628.2:c.2157C>G
  • NM_001354629.2:c.2151C>G
  • NM_001354630.2:c.2085C>G
  • NP_000240.1:p.Tyr750Ter
  • NP_000240.1:p.Tyr750Ter
  • NP_001161089.1:p.Tyr652Ter
  • NP_001161090.1:p.Tyr509Ter
  • NP_001161091.1:p.Tyr509Ter
  • NP_001245200.1:p.Tyr681Ter
  • NP_001245202.1:p.Tyr509Ter
  • NP_001245203.1:p.Tyr509Ter
  • NP_001341544.1:p.Tyr509Ter
  • NP_001341545.1:p.Tyr509Ter
  • NP_001341546.1:p.Tyr509Ter
  • NP_001341547.1:p.Tyr509Ter
  • NP_001341548.1:p.Tyr509Ter
  • NP_001341549.1:p.Tyr652Ter
  • NP_001341550.1:p.Tyr409Ter
  • NP_001341551.1:p.Tyr409Ter
  • NP_001341552.1:p.Tyr409Ter
  • NP_001341553.1:p.Tyr392Ter
  • NP_001341554.1:p.Tyr392Ter
  • NP_001341555.1:p.Tyr392Ter
  • NP_001341556.1:p.Tyr392Ter
  • NP_001341557.1:p.Tyr719Ter
  • NP_001341558.1:p.Tyr717Ter
  • NP_001341559.1:p.Tyr695Ter
  • LRG_216t1:c.2250C>G
  • LRG_216:g.62283C>G
  • LRG_216p1:p.Tyr750Ter
  • NC_000003.11:g.37092123C>G
  • NM_000249.3:c.2250C>G
  • p.Tyr750*
Protein change:
Y392*
Links:
dbSNP: rs267607893
NCBI 1000 Genomes Browser:
rs267607893
Molecular consequence:
  • NM_000249.4:c.2250C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001167617.3:c.1956C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001167618.3:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001167619.3:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001258271.2:c.2043C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001258273.2:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001258274.3:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354615.2:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354616.2:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354617.2:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354618.2:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354619.2:c.1527C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354620.2:c.1956C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354621.2:c.1227C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354622.2:c.1227C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354623.2:c.1227C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354624.2:c.1176C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354625.2:c.1176C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354626.2:c.1176C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354627.2:c.1176C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354628.2:c.2157C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354629.2:c.2151C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354630.2:c.2085C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000565173GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Likely pathogenic
(Jul 2, 2015)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000565173.4

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

Description

This variant is denoted MLH1 c.2250C>G at the cDNA level and p.Tyr750Ter (Y750X) at the protein level. The substitution creates a nonsense variant, which changes a Tyrosine to a premature stop codon (TAC>TAG). This variant is, the last exon of the gene, and results in protein truncation and loss of 7 amino acids. MLH1 Tyr750Ter has been observed in at least two individuals with colorectal cancer and in at least one HNPCC family (Syngal 1999, Wang 2006, Mueller 2009). In a mouse embryonic fibroblast model, this variant was associated with MLH1 expression levels similar to wild type, but reduced levels of PMS2, which was described as indicating an inability to stabilize PMS2 protein (Mohd 2006). Similar results were also demonstrated in an in vitro human cell line study, which further reported that MLH1 Tyr750Ter was associated with significantly reduced, but not entirely eliminated, mismatch repair activity (Kosinski 2010). We therefore consider MLH1 Tyr750Ter to be a likely pathogenic variant.

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

Last Updated: May 1, 2024