U.S. flag

An official website of the United States government

NM_000249.4(MLH1):c.157G>T (p.Glu53Ter) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 28, 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:
RCV001799562.3

Allele description [Variation Report for NM_000249.4(MLH1):c.157G>T (p.Glu53Ter)]

NM_000249.4(MLH1):c.157G>T (p.Glu53Ter)

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.157G>T (p.Glu53Ter)
HGVS:
  • NC_000003.12:g.36996659G>T
  • NG_007109.2:g.8310G>T
  • NG_008418.1:g.1646C>A
  • NM_000249.4:c.157G>TMANE SELECT
  • NM_001167617.3:c.-133G>T
  • NM_001167618.3:c.-567G>T
  • NM_001167619.3:c.-475G>T
  • NM_001258271.2:c.157G>T
  • NM_001258273.2:c.-517+2996G>T
  • NM_001258274.3:c.-712G>T
  • NM_001354615.2:c.-470G>T
  • NM_001354616.2:c.-475G>T
  • NM_001354617.2:c.-567G>T
  • NM_001354618.2:c.-567G>T
  • NM_001354619.2:c.-567G>T
  • NM_001354620.2:c.-133G>T
  • NM_001354621.2:c.-660G>T
  • NM_001354622.2:c.-773G>T
  • NM_001354623.2:c.-723+2769G>T
  • NM_001354624.2:c.-670G>T
  • NM_001354625.2:c.-573G>T
  • NM_001354626.2:c.-670G>T
  • NM_001354627.2:c.-670G>T
  • NM_001354628.2:c.157G>T
  • NM_001354629.2:c.157G>T
  • NM_001354630.2:c.157G>T
  • NP_000240.1:p.Glu53Ter
  • NP_001245200.1:p.Glu53Ter
  • NP_001341557.1:p.Glu53Ter
  • NP_001341558.1:p.Glu53Ter
  • NP_001341559.1:p.Glu53Ter
  • LRG_216:g.8310G>T
  • NC_000003.11:g.37038150G>T
Protein change:
E53*
Molecular consequence:
  • NM_001167617.3:c.-133G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-567G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-475G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-712G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354615.2:c.-470G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354616.2:c.-475G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354617.2:c.-567G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-567G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-567G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354620.2:c.-133G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-660G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-773G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354624.2:c.-670G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354625.2:c.-573G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354626.2:c.-670G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-670G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258273.2:c.-517+2996G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.-723+2769G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.4:c.157G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001258271.2:c.157G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354628.2:c.157G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354629.2:c.157G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354630.2:c.157G>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Muir-Torré syndrome (MRTES)
Synonyms:
Muir-Torre syndrome; Cutaneous sebaceous neoplasms and keratoacanthomas multiple with gastrointestinal and other carcinomas; MSH2-Related Muir-Torre Syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008018; MedGen: C1321489; Orphanet: 587; OMIM: 158320
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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002043771Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 28, 2021) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes11not providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV002043771.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.157G>T variant is not present in publicly available population databases like 1000 Genomes, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC) and Genome Aggregation Database (gnomAD). The variant is not present in Indian Exome Database and in our in-house exome database. The variant was not earlier reported to ClinVar, Human Genome Mutation Database (HGMD) and OMIM databases in any affected individuals. In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome, InterVar etc. predicted this variant to be likely deletorouis.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot provideddiscovery1not provided1not provided

Last Updated: Aug 5, 2023