NM_000249.4(MLH1):c.565G>C (p.Gly189Arg) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 20, 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:: RCV003014363.3

Allele description [Variation Report for NM_000249.4(MLH1):c.565G>C (p.Gly189Arg)]

NM_000249.4(MLH1):c.565G>C (p.Gly189Arg)

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.565G>C (p.Gly189Arg)

HGVS:

NC_000003.12:g.37011839G>C
NG_007109.2:g.23490G>C
NM_000249.4:c.565G>CMANE SELECT
NM_001167617.3:c.271G>C
NM_001167618.3:c.-159G>C
NM_001167619.3:c.-159G>C
NM_001258271.2:c.565G>C
NM_001258273.2:c.-159G>C
NM_001258274.3:c.-159G>C
NM_001354615.2:c.-159G>C
NM_001354616.2:c.-159G>C
NM_001354617.2:c.-159G>C
NM_001354618.2:c.-159G>C
NM_001354619.2:c.-159G>C
NM_001354620.2:c.271G>C
NM_001354621.2:c.-252G>C
NM_001354622.2:c.-365G>C
NM_001354623.2:c.-365G>C
NM_001354624.2:c.-262G>C
NM_001354625.2:c.-262G>C
NM_001354626.2:c.-262G>C
NM_001354627.2:c.-262G>C
NM_001354628.2:c.565G>C
NM_001354629.2:c.466G>C
NM_001354630.2:c.565G>C
NP_000240.1:p.Gly189Arg
NP_000240.1:p.Gly189Arg
NP_001161089.1:p.Gly91Arg
NP_001245200.1:p.Gly189Arg
NP_001341549.1:p.Gly91Arg
NP_001341557.1:p.Gly189Arg
NP_001341558.1:p.Gly156Arg
NP_001341559.1:p.Gly189Arg
LRG_216t1:c.565G>C
LRG_216:g.23490G>C
LRG_216p1:p.Gly189Arg
NC_000003.11:g.37053330G>C
NM_000249.3:c.565G>C

Protein change:

G156R

Molecular consequence:

NM_001167618.3:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-159G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-252G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-365G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-365G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-262G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-262G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-262G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-262G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.565G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001167617.3:c.271G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.565G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354620.2:c.271G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.565G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.466G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.565G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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Mus musculus netrin 4 (Ntn4), mRNA
Mus musculus netrin 4 (Ntn4), mRNA
gi|10946625|ref|NM_021320.1|

Nucleotide
ACSL1 [Tupaia chinensis]
ACSL1 [Tupaia chinensis]
Gene ID:102475321

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003317229	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 20, 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

SCV003317229

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 20, 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, SCV003317229.2

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C65"). 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 glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 189 of the MLH1 protein (p.Gly189Arg).

#	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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