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NM_000249.4(MLH1):c.169A>T (p.Lys57Ter) AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 11, 2023
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:
RCV003454273.1

Allele description [Variation Report for NM_000249.4(MLH1):c.169A>T (p.Lys57Ter)]

NM_000249.4(MLH1):c.169A>T (p.Lys57Ter)

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.169A>T (p.Lys57Ter)
HGVS:
  • NC_000003.12:g.36996671A>T
  • NG_007109.2:g.8322A>T
  • NG_008418.1:g.1634T>A
  • NM_000249.4:c.169A>TMANE SELECT
  • NM_001167617.3:c.-121A>T
  • NM_001167618.3:c.-555A>T
  • NM_001167619.3:c.-463A>T
  • NM_001258271.2:c.169A>T
  • NM_001258273.2:c.-517+3008A>T
  • NM_001258274.3:c.-700A>T
  • NM_001354615.2:c.-458A>T
  • NM_001354616.2:c.-463A>T
  • NM_001354617.2:c.-555A>T
  • NM_001354618.2:c.-555A>T
  • NM_001354619.2:c.-555A>T
  • NM_001354620.2:c.-121A>T
  • NM_001354621.2:c.-648A>T
  • NM_001354622.2:c.-761A>T
  • NM_001354623.2:c.-723+2781A>T
  • NM_001354624.2:c.-658A>T
  • NM_001354625.2:c.-561A>T
  • NM_001354626.2:c.-658A>T
  • NM_001354627.2:c.-658A>T
  • NM_001354628.2:c.169A>T
  • NM_001354629.2:c.169A>T
  • NM_001354630.2:c.169A>T
  • NP_000240.1:p.Lys57Ter
  • NP_000240.1:p.Lys57Ter
  • NP_001245200.1:p.Lys57Ter
  • NP_001341557.1:p.Lys57Ter
  • NP_001341558.1:p.Lys57Ter
  • NP_001341559.1:p.Lys57Ter
  • LRG_216t1:c.169A>T
  • LRG_216:g.8322A>T
  • LRG_216p1:p.Lys57Ter
  • NC_000003.11:g.37038162A>T
  • NM_000249.3:c.169A>T
Protein change:
K57*
Molecular consequence:
  • NM_001167617.3:c.-121A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-555A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-463A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-700A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354615.2:c.-458A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354616.2:c.-463A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354617.2:c.-555A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-555A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-555A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354620.2:c.-121A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-648A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-761A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354624.2:c.-658A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354625.2:c.-561A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354626.2:c.-658A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-658A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258273.2:c.-517+3008A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.-723+2781A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.4:c.169A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001258271.2:c.169A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354628.2:c.169A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354629.2:c.169A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354630.2:c.169A>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Colorectal cancer, hereditary nonpolyposis, type 2 (LYNCH2)
Synonyms:
COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 2; Lynch syndrome II; 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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004186329Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))		Pathogenic
(Jul 11, 2023) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV004186329.1

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

Description

This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.

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

Last Updated: May 1, 2024