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NM_000249.4(MLH1):c.154A>T (p.Lys52Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 1, 2021
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:
RCV002403333.2

Allele description [Variation Report for NM_000249.4(MLH1):c.154A>T (p.Lys52Ter)]

NM_000249.4(MLH1):c.154A>T (p.Lys52Ter)

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.154A>T (p.Lys52Ter)
HGVS:
  • NC_000003.12:g.36996656A>T
  • NG_007109.2:g.8307A>T
  • NG_008418.1:g.1649T>A
  • NM_000249.4:c.154A>TMANE SELECT
  • NM_001167617.3:c.-136A>T
  • NM_001167618.3:c.-570A>T
  • NM_001167619.3:c.-478A>T
  • NM_001258271.2:c.154A>T
  • NM_001258273.2:c.-517+2993A>T
  • NM_001258274.3:c.-715A>T
  • NM_001354615.2:c.-473A>T
  • NM_001354616.2:c.-478A>T
  • NM_001354617.2:c.-570A>T
  • NM_001354618.2:c.-570A>T
  • NM_001354619.2:c.-570A>T
  • NM_001354620.2:c.-136A>T
  • NM_001354621.2:c.-663A>T
  • NM_001354622.2:c.-776A>T
  • NM_001354623.2:c.-723+2766A>T
  • NM_001354624.2:c.-673A>T
  • NM_001354625.2:c.-576A>T
  • NM_001354626.2:c.-673A>T
  • NM_001354627.2:c.-673A>T
  • NM_001354628.2:c.154A>T
  • NM_001354629.2:c.154A>T
  • NM_001354630.2:c.154A>T
  • NP_000240.1:p.Lys52Ter
  • NP_000240.1:p.Lys52Ter
  • NP_001245200.1:p.Lys52Ter
  • NP_001341557.1:p.Lys52Ter
  • NP_001341558.1:p.Lys52Ter
  • NP_001341559.1:p.Lys52Ter
  • LRG_216t1:c.154A>T
  • LRG_216:g.8307A>T
  • LRG_216p1:p.Lys52Ter
  • NC_000003.11:g.37038147A>T
  • NM_000249.3:c.154A>T
Protein change:
K52*
Molecular consequence:
  • NM_001167617.3:c.-136A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-570A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-478A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-715A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354615.2:c.-473A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354616.2:c.-478A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354617.2:c.-570A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-570A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-570A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354620.2:c.-136A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-663A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-776A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354624.2:c.-673A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354625.2:c.-576A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354626.2:c.-673A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-673A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258273.2:c.-517+2993A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.-723+2766A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.4:c.154A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001258271.2:c.154A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354628.2:c.154A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354629.2:c.154A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354630.2:c.154A>T - nonsense - [Sequence Ontology: SO:0001587]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002707436Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Jun 1, 2021) 		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, SCV002707436.2

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

Description

The p.K52* pathogenic mutation (also known as c.154A>T), located in coding exon 2 of the MLH1 gene, results from an A to T substitution at nucleotide position 154. This changes the amino acid from a lysine to a stop codon within coding exon 2. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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

Last Updated: May 1, 2024