NM_000249.4(MLH1):c.425G>T (p.Cys142Phe) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 27, 2019
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:: RCV001039753.4

Allele description [Variation Report for NM_000249.4(MLH1):c.425G>T (p.Cys142Phe)]

NM_000249.4(MLH1):c.425G>T (p.Cys142Phe)

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.425G>T (p.Cys142Phe)

HGVS:

NC_000003.12:g.37007035G>T
NG_007109.2:g.18686G>T
NM_000249.4:c.425G>TMANE SELECT
NM_001167617.3:c.131G>T
NM_001167618.3:c.-299G>T
NM_001167619.3:c.-207G>T
NM_001258271.2:c.425G>T
NM_001258273.2:c.-299G>T
NM_001258274.3:c.-299G>T
NM_001354615.2:c.-207G>T
NM_001354616.2:c.-207G>T
NM_001354617.2:c.-299G>T
NM_001354618.2:c.-299G>T
NM_001354619.2:c.-299G>T
NM_001354620.2:c.131G>T
NM_001354621.2:c.-392G>T
NM_001354622.2:c.-505G>T
NM_001354623.2:c.-505G>T
NM_001354624.2:c.-402G>T
NM_001354625.2:c.-310G>T
NM_001354626.2:c.-402G>T
NM_001354627.2:c.-402G>T
NM_001354628.2:c.425G>T
NM_001354629.2:c.326G>T
NM_001354630.2:c.425G>T
NP_000240.1:p.Cys142Phe
NP_001161089.1:p.Cys44Phe
NP_001245200.1:p.Cys142Phe
NP_001341549.1:p.Cys44Phe
NP_001341557.1:p.Cys142Phe
NP_001341558.1:p.Cys109Phe
NP_001341559.1:p.Cys142Phe
LRG_216t1:c.425G>T
LRG_216:g.18686G>T
NC_000003.11:g.37048526G>T
NM_000249.3:c.425G>T

Protein change:

C109F

Links:

dbSNP: rs1553642098

NCBI 1000 Genomes Browser:

rs1553642098

Molecular consequence:

NM_001167618.3:c.-299G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-207G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-299G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-299G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-207G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-207G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-299G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-299G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-299G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-392G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-505G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-505G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-402G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-310G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-402G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-402G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.425G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001167617.3:c.131G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.425G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354620.2:c.131G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.425G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.326G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.425G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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drebrin-like protein isoform d [Homo sapiens]
drebrin-like protein isoform d [Homo sapiens]
gi|546231336|ref|NP_001271242.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001203299	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 27, 2019)	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

SCV001203299

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 27, 2019)

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, SCV001203299.4

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

Description

This variant is not present in population databases (ExAC no frequency). This sequence change replaces cysteine with phenylalanine at codon 142 of the MLH1 protein (p.Cys142Phe). The cysteine residue is highly conserved and there is a large physicochemical difference between cysteine and phenylalanine. This variant has not been reported in the literature in individuals with MLH1-related conditions. 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: "Probably Damaging"; Align-GVGD: "Class C0").

#	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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