NM_000249.4(MLH1):c.206G>C (p.Arg69Thr) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 6, 2022
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:: RCV000629715.4

Allele description [Variation Report for NM_000249.4(MLH1):c.206G>C (p.Arg69Thr)]

NM_000249.4(MLH1):c.206G>C (p.Arg69Thr)

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.206G>C (p.Arg69Thr)

HGVS:

NC_000003.12:g.36996708G>C
NG_007109.2:g.8359G>C
NG_008418.1:g.1597C>G
NM_000249.4:c.206G>CMANE SELECT
NM_001167617.3:c.-84G>C
NM_001167618.3:c.-518G>C
NM_001167619.3:c.-426G>C
NM_001258271.2:c.206G>C
NM_001258273.2:c.-517+3045G>C
NM_001258274.3:c.-663G>C
NM_001354615.2:c.-421G>C
NM_001354616.2:c.-426G>C
NM_001354617.2:c.-518G>C
NM_001354618.2:c.-518G>C
NM_001354619.2:c.-518G>C
NM_001354620.2:c.-84G>C
NM_001354621.2:c.-611G>C
NM_001354622.2:c.-724G>C
NM_001354623.2:c.-723+2818G>C
NM_001354624.2:c.-621G>C
NM_001354625.2:c.-524G>C
NM_001354626.2:c.-621G>C
NM_001354627.2:c.-621G>C
NM_001354628.2:c.206G>C
NM_001354629.2:c.206G>C
NM_001354630.2:c.206G>C
NP_000240.1:p.Arg69Thr
NP_000240.1:p.Arg69Thr
NP_001245200.1:p.Arg69Thr
NP_001341557.1:p.Arg69Thr
NP_001341558.1:p.Arg69Thr
NP_001341559.1:p.Arg69Thr
LRG_216t1:c.206G>C
LRG_216:g.8359G>C
LRG_216p1:p.Arg69Thr
NC_000003.11:g.37038199G>C
NM_000249.3:c.206G>C

Protein change:

R69T

Links:

dbSNP: rs63751661

NCBI 1000 Genomes Browser:

rs63751661

Molecular consequence:

NM_001167617.3:c.-84G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-518G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-426G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-663G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-421G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-426G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-518G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-518G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-518G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-84G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-611G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-724G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-621G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-524G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-621G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-621G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-517+3045G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354623.2:c.-723+2818G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000249.4:c.206G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.206G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.206G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.206G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.206G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

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Microbe sample from Chloroflexota bacterium
Microbe sample from Chloroflexota bacterium

biosample
Microbe sample from Candidatus Saccharibacteria bacterium
Microbe sample from Candidatus Saccharibacteria bacterium

biosample
Bovine viral diarrhea virus 1 isolate BSC-4 E2 gene, partial cds
Bovine viral diarrhea virus 1 isolate BSC-4 E2 gene, partial cds
gi|1685826268|gb|MK170076.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000750671	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 6, 2022)	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

SCV000750671

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 6, 2022)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000750671.3

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 525612). This variant has not been reported in the literature in individuals affected with MLH1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with threonine, which is neutral and polar, at codon 69 of the MLH1 protein (p.Arg69Thr). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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