NM_000249.4:c.644A>G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP6

The NM_000249.4(MLH1):c.644A>G(p.Asn215Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000185 in 1,461,728 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N215T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

MLH1
NM_000249.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:5B:3

Conservation

PhyloP100: 8.86

Publications

8 publications found

Variant links:

Genes affected

MLH1 (HGNC:7127): (mutL homolog 1) The protein encoded by this gene can heterodimerize with mismatch repair endonuclease PMS2 to form MutL alpha, part of the DNA mismatch repair system. When MutL alpha is bound by MutS beta and some accessory proteins, the PMS2 subunit of MutL alpha introduces a single-strand break near DNA mismatches, providing an entry point for exonuclease degradation. The encoded protein is also involved in DNA damage signaling and can heterodimerize with DNA mismatch repair protein MLH3 to form MutL gamma, which is involved in meiosis. This gene was identified as a locus frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). [provided by RefSeq, Aug 2017]

MLH1 Gene-Disease associations (from GenCC):

Lynch syndrome
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, ClinGen, Orphanet
Lynch syndrome 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp
Muir-Torre syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, G2P, Orphanet
mismatch repair cancer syndrome 1
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
Lynch syndrome 1
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
ovarian cancer
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
malignant pancreatic neoplasm
Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
rhabdomyosarcoma
Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
prostate cancer
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
breast cancer
Inheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
hereditary breast carcinoma
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

MLH1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP6

Variant 3-37012066-A-G is Benign according to our data. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301. Variant chr3-37012066-A-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 90301.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4 link	c.644A>G	p.Asn215Ser	missense_variant	Exon 8 of 19	ENST00000231790.8	NP_000240.1	P40692-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8 link	c.644A>G	p.Asn215Ser	missense_variant	Exon 8 of 19	1	NM_000249.4	ENSP00000231790.3		P40692-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000319

AC:

AN:

251154

AF XY:

0.0000368

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000185

AC:

AN:

1461728

Hom.:

Cov.:

AF XY:

0.0000220

AC XY:

AN XY:

727178

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26132

East Asian (EAS)

AF:

0.00

AC:

AN:

39690

South Asian (SAS)

AF:

0.000301

AC:

AN:

86256

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53416

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

8.99e-7

AC:

AN:

1111878

Other (OTH)

AF:

0.00

AC:

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000426

Hom.:

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:5Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome

Uncertain:1Benign:1

Nov 19, 2021

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Jan 26, 2023

Color Diagnostics, LLC DBA Color Health

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This missense variant replaces asparagine with serine at codon 215 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). A functional study reported that this variant had a normal DNA damage response in an MLH1-null human cell line (PMID: 30998989). This variant has been reported in an individual from a Lynch syndrome family (PMID: 18561205) and in an individual affected with peritoneum cancer (PMID: 30093976). This variant has been identified in 8/251154 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

not specified

Uncertain:1

Jul 06, 2017

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Colorectal cancer, hereditary nonpolyposis, type 2

Uncertain:1

Jan 11, 2024

Baylor Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Lynch syndrome

Uncertain:1

Mar 07, 2023

All of Us Research Program, National Institutes of Health

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This missense variant replaces asparagine with serine at codon 215 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. A functional study reported that this variant had a normal DNA damage response in an MLH1-null human cell line (PMID: 30998989). This variant has been reported in an individual from a Lynch syndrome family (PMID: 18561205 and the UMD database). This variant has been identified in 8/251154 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

not provided

Uncertain:1

Feb 12, 2024

GeneDx

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies suggest a neutral effect: demonstrates cell survival comparable to other known neutral variants in a methylation tolerance assay (PMID: 30998989); This variant is associated with the following publications: (PMID: 30093976, 26333163, 18561205, 22753075, 30998989) -

Hereditary nonpolyposis colon cancer

Benign:1

Apr 09, 2024

Mendelics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hereditary nonpolyposis colorectal neoplasms

Benign:1

Jan 06, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.064

BayesDel_noAF

Uncertain

-0.060

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.69

D;.

Eigen

Uncertain

0.59

Eigen_PC

Uncertain

0.66

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.96

D;D

M_CAP

Uncertain

0.12

MetaRNN

Uncertain

0.73

D;D

MetaSVM

Uncertain

0.086

MutationAssessor

Uncertain

2.2

M;.

PhyloP100

8.9

PrimateAI

Uncertain

0.54

PROVEAN

Uncertain

-2.8

D;D

REVEL

Uncertain

0.61

Sift

Uncertain

0.028

D;D

Sift4G

Uncertain

0.057

T;D

Polyphen

0.61

P;.

Vest4

0.73

MutPred

0.50

Gain of phosphorylation at N215 (P = 0.0889);.;

MVP

0.84

MPC

0.30

ClinPred

0.70

GERP RS

5.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.74

gMVP

0.72

Mutation Taster

=247/53

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

Splicevardb

1.0

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over