NM_000249.4(MLH1):c.644A>C (p.Asn215Thr) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 11, 2020
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:: RCV001928352.6

Allele description [Variation Report for NM_000249.4(MLH1):c.644A>C (p.Asn215Thr)]

NM_000249.4(MLH1):c.644A>C (p.Asn215Thr)

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.644A>C (p.Asn215Thr)

HGVS:

NC_000003.12:g.37012066A>C
NG_007109.2:g.23717A>C
NM_000249.3:c.644A>C
NM_000249.4:c.644A>CMANE SELECT
NM_001167617.3:c.350A>C
NM_001167618.3:c.-80A>C
NM_001167619.3:c.-80A>C
NM_001258271.2:c.644A>C
NM_001258273.2:c.-80A>C
NM_001258274.3:c.-80A>C
NM_001354615.2:c.-80A>C
NM_001354616.2:c.-80A>C
NM_001354617.2:c.-80A>C
NM_001354618.2:c.-80A>C
NM_001354619.2:c.-80A>C
NM_001354620.2:c.350A>C
NM_001354621.2:c.-173A>C
NM_001354622.2:c.-286A>C
NM_001354623.2:c.-286A>C
NM_001354624.2:c.-183A>C
NM_001354625.2:c.-183A>C
NM_001354626.2:c.-183A>C
NM_001354627.2:c.-183A>C
NM_001354628.2:c.644A>C
NM_001354629.2:c.545A>C
NM_001354630.2:c.644A>C
NP_000240.1:p.Asn215Thr
NP_001161089.1:p.Asn117Thr
NP_001245200.1:p.Asn215Thr
NP_001341549.1:p.Asn117Thr
NP_001341557.1:p.Asn215Thr
NP_001341558.1:p.Asn182Thr
NP_001341559.1:p.Asn215Thr
LRG_216t1:c.644A>C
LRG_216:g.23717A>C
NC_000003.11:g.37053557A>C

Protein change:

N117T

Links:

dbSNP: rs267607775

NCBI 1000 Genomes Browser:

rs267607775

Molecular consequence:

NM_001167618.3:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-80A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-173A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-286A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-286A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-183A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-183A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-183A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-183A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.644A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001167617.3:c.350A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.644A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354620.2:c.350A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.644A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.545A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.644A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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GDPD1 [Rhinolophus ferrumequinum]
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002178760	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 11, 2020)	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

SCV002178760

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 11, 2020)

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, SCV002178760.3

#	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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MLH1 protein function. This variant has not been reported in the literature in individuals with MLH1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces asparagine with threonine at codon 215 of the MLH1 protein (p.Asn215Thr). The asparagine residue is highly conserved and there is a small physicochemical difference between asparagine and threonine.

#	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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