NM_000249.4(MLH1):c.196A>G (p.Thr66Ala) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 4, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000220302.5

Allele description [Variation Report for NM_000249.4(MLH1):c.196A>G (p.Thr66Ala)]

NM_000249.4(MLH1):c.196A>G (p.Thr66Ala)

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.196A>G (p.Thr66Ala)

HGVS:

NC_000003.12:g.36996698A>G
NG_007109.2:g.8349A>G
NG_008418.1:g.1607T>C
NM_000249.4:c.196A>GMANE SELECT
NM_001167617.3:c.-94A>G
NM_001167618.3:c.-528A>G
NM_001167619.3:c.-436A>G
NM_001258271.2:c.196A>G
NM_001258273.2:c.-517+3035A>G
NM_001258274.3:c.-673A>G
NM_001354615.2:c.-431A>G
NM_001354616.2:c.-436A>G
NM_001354617.2:c.-528A>G
NM_001354618.2:c.-528A>G
NM_001354619.2:c.-528A>G
NM_001354620.2:c.-94A>G
NM_001354621.2:c.-621A>G
NM_001354622.2:c.-734A>G
NM_001354623.2:c.-723+2808A>G
NM_001354624.2:c.-631A>G
NM_001354625.2:c.-534A>G
NM_001354626.2:c.-631A>G
NM_001354627.2:c.-631A>G
NM_001354628.2:c.196A>G
NM_001354629.2:c.196A>G
NM_001354630.2:c.196A>G
NP_000240.1:p.Thr66Ala
NP_000240.1:p.Thr66Ala
NP_001245200.1:p.Thr66Ala
NP_001341557.1:p.Thr66Ala
NP_001341558.1:p.Thr66Ala
NP_001341559.1:p.Thr66Ala
LRG_216t1:c.196A>G
LRG_216:g.8349A>G
LRG_216p1:p.Thr66Ala
NC_000003.11:g.37038189A>G
NM_000249.3:c.196A>G

Protein change:

T66A

Links:

dbSNP: rs876660926

NCBI 1000 Genomes Browser:

rs876660926

Molecular consequence:

NM_001167617.3:c.-94A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-528A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-436A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-673A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-431A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-436A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-528A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-528A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-528A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-94A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-621A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-734A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-631A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-534A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-631A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-631A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-517+3035A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001354623.2:c.-723+2808A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000249.4:c.196A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.196A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.196A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.196A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.196A>G - missense variant - [Sequence Ontology: SO:0001583]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000278738	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Oct 7, 2015)	germline	clinical testing	Citation Link,
SCV000904837	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 4, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000278738

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Oct 7, 2015)

germline

clinical testing

Citation Link,

SCV000904837

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 4, 2018)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Ambry Genetics, SCV000278738.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The p.T66A variant (also known as c.196A>G), located in coding exon 2 of the MLH1 gene, results from an A to G substitution at nucleotide position 196. The threonine at codon 66 is replaced by alanine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Color Diagnostics, LLC DBA Color Health, SCV000904837.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 7, 2024

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