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NM_000249.4(MLH1):c.198C>T (p.Thr66=) AND Lynch syndrome

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Sep 5, 2013
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV000075463.8

Allele description [Variation Report for NM_000249.4(MLH1):c.198C>T (p.Thr66=)]

NM_000249.4(MLH1):c.198C>T (p.Thr66=)

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.198C>T (p.Thr66=)
Other names:
p.T66T:ACC>ACT
HGVS:
  • NC_000003.12:g.36996700C>T
  • NG_007109.2:g.8351C>T
  • NG_008418.1:g.1605G>A
  • NM_000249.4:c.198C>TMANE SELECT
  • NM_001167617.3:c.-92C>T
  • NM_001167618.3:c.-526C>T
  • NM_001167619.3:c.-434C>T
  • NM_001258271.2:c.198C>T
  • NM_001258273.2:c.-517+3037C>T
  • NM_001258274.3:c.-671C>T
  • NM_001354615.2:c.-429C>T
  • NM_001354616.2:c.-434C>T
  • NM_001354617.2:c.-526C>T
  • NM_001354618.2:c.-526C>T
  • NM_001354619.2:c.-526C>T
  • NM_001354620.2:c.-92C>T
  • NM_001354621.2:c.-619C>T
  • NM_001354622.2:c.-732C>T
  • NM_001354623.2:c.-723+2810C>T
  • NM_001354624.2:c.-629C>T
  • NM_001354625.2:c.-532C>T
  • NM_001354626.2:c.-629C>T
  • NM_001354627.2:c.-629C>T
  • NM_001354628.2:c.198C>T
  • NM_001354629.2:c.198C>T
  • NM_001354630.2:c.198C>T
  • NP_000240.1:p.Thr66=
  • NP_000240.1:p.Thr66=
  • NP_001245200.1:p.Thr66=
  • NP_001341557.1:p.Thr66=
  • NP_001341558.1:p.Thr66=
  • NP_001341559.1:p.Thr66=
  • LRG_216t1:c.198C>T
  • LRG_216:g.8351C>T
  • LRG_216p1:p.Thr66=
  • NC_000003.11:g.37038191C>T
  • NM_000249.3:c.198C>T
  • p.T66T
Links:
dbSNP: rs61751642
NCBI 1000 Genomes Browser:
rs61751642
Molecular consequence:
  • NM_001167617.3:c.-92C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-526C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-434C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-671C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354615.2:c.-429C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354616.2:c.-434C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354617.2:c.-526C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-526C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-526C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354620.2:c.-92C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-619C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-732C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354624.2:c.-629C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354625.2:c.-532C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354626.2:c.-629C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-629C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258273.2:c.-517+3037C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.-723+2810C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.4:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001258271.2:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354628.2:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354629.2:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354630.2:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
104

Condition(s)

Name:
Lynch syndrome
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000106460International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
reviewed by expert panel

(Guidelines v1.9)		Likely benign
(Sep 5, 2013) 		germlineresearch

Citation Link,

SCV004835250All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(Feb 5, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown104not providednot provided108544not providedclinical testing, research

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 International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000106460.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

Synonymous substitution with no effect on splicing & MAF 0.01-1%

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

From All of Us Research Program, National Institutes of Health, SCV004835250.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided104not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided104not providednot providednot provided

Last Updated: Oct 20, 2024