rs63751711
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM2PM5PP3PP5_Very_Strong
The ENST00000231790.8(MLH1):c.677G>A(p.Arg226Gln) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,452,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R226L) has been classified as Likely pathogenic.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
MLH1
ENST00000231790.8 missense, splice_region
ENST00000231790.8 missense, splice_region
Scores
9
6
4
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 7.59
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 13 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr3-37012099-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 90319.Status of the report is reviewed_by_expert_panel, 3 stars.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.801
PP5
Variant 3-37012099-G-A is Pathogenic according to our data. Variant chr3-37012099-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 90318.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37012099-G-A is described in Lovd as [Pathogenic]. Variant chr3-37012099-G-A is described in Lovd as [Benign]. Variant chr3-37012099-G-A is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MLH1 | NM_000249.4 | c.677G>A | p.Arg226Gln | missense_variant, splice_region_variant | 8/19 | ENST00000231790.8 | NP_000240.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MLH1 | ENST00000231790.8 | c.677G>A | p.Arg226Gln | missense_variant, splice_region_variant | 8/19 | 1 | NM_000249.4 | ENSP00000231790 | P1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1452078Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 722968
GnomAD4 exome
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GnomAD4 genome
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32
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:21
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Lynch syndrome Pathogenic:5
| Pathogenic, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Mar 04, 2024 | The consequence of the MLH1 c.677G>A variant change is to alter splicing, so at the amino acid level can also be described as p.Gln197ArgfsX8, as cited in the literature. This variant alters the last nucleotide of exon 8 and results in abnormal splicing. Aberrant splicing and/or loss of function is an established mechanism of disease. This prediction has been confirmed by RNA studies (PMID: 9777949, 18561205). A different variant that results in the same missense substitution has been reported in association with disease and is independently classified as likely pathogenic. This variant has been reported in multiple individuals with Lynch syndrome (PMID: 8571956, 12624141, 15309712, 17453009). This variant is absent from or rare in large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This variant has been reported to co-segregate with disease in more than one family (PMID: 16341550, 15300854, 12547705). - |
| Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | Jul 02, 2018 | - - |
| Pathogenic, reviewed by expert panel | research | International Society for Gastrointestinal Hereditary Tumours (InSiGHT) | Sep 05, 2013 | Variant causes splicing aberration leading to truncated protein: full inactivation of variant allele - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Oct 20, 2017 | Variant summary: The MLH1 c.677G>A (p.Arg226Gln) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). 4/5 splice prediction tools predict a significant impact on normal splicing. These predictions were also confirmed by functional studies, showing that the variant which is located at the last nucleotide of exon 8, disrupts the splice donor site and leads to skipping of exon 8, resulting in a frameshift with a consequential stop codon (Sharp 2004, Pagenstecher 2006, Tournier2008). Although the variant can be found in the literature under the name of p.Arg226Gln, the consequence of the variant nucleotide change at the amino acid level is more properly described as p.Gln197ArgfsX8, as cited in the literature (Moussa 2011, Lagerstedt-Robinson 2016). The variant has been reported in several individuals with Lynch syndrome tumors, with cases of confirmed co-segregation data (Wijnen 1996, de Jong 2004, Sharp 2004, Pagenstecher 2006, Moussa 2011, Lagerstedt-Robinson 2016). This variant is absent in 245866 control chromosomes. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | research | A.C.Camargo Cancer Center / LGBM, A.C.Camargo Cancer Center | Jan 30, 2019 | - - |
not provided Pathogenic:5
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Mar 23, 2021 | This variant has been described as pathogenic and/or having a deleterious effect on MLH1 protein function in the published literature by compromising normal splicing and resulting in the skipping of exon 8 (PMID: 15300854 (2004), 16341550 (2006), and 18561205 (2008)). This variant has been identified in patients with a personal and/or family history consistent with Lynch syndrome (PMID: 17453009 (2007), 25980754 (2015), and 27601186 (2016)). Based on the available information, this variant is classified as pathogenic. - |
| Pathogenic, no assertion criteria provided | research | Mayo Clinic Laboratories, Mayo Clinic | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Feb 02, 2024 | Protein and RNA-based functional studies show that this variant disrupts the adjacent natural splice donor site leading to skipping of exon 8, resulting in a frameshift (PMID: 9777949, 15300854, 16341550, 18561205); Observed in several individuals meeting Amsterdam criteria, segregating with disease in at least two kindreds, and with most studied tumors demonstrating microsatellite instability and/or loss of MLH1 expression (PMID: 8571956, 12373605, 12547705, 14871975, 17054581, 17453009, 27435373, 29237405, 27696107); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 19690142, 27601186, 12624141, 27696107, 26078562, 19248199, 32980694, 31830689, 28888541, 29758216, 25980754, 25430799, 8571956, 15200905, 16736289, 16341550, 18561205, 9311737, 12373605, 23760103, 15300854, 12547705, 17453009, 15778432, 14871975, 10422993, 12067992, 17054581, 17569143, 18692554, 11524701, 21034533, 12740349, 24362816, 26248088, 25892863, 26300997, 27435373, 28643016, 28127413, 29237405, 28874130, 27978560, 22290698, 28596308, 12362047, 17192056, 34178123, 29505604, 9777949, 30787465, 28932927, 29575718, 30521064, 29887214, 22753075) - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 10, 2022 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - |  The MLH1 p.Arg226Gln variant was identified in 15 of 4876 proband chromosomes (frequency: 0.003) from individuals or families with Lynch Syndrome or  HNPCC  (Papp 2007, Spaepen 2006, Pagenstecher 2006, Dominguez-Valentin 2016, Gille 2002, Lagerstedt-Robinson 2016, Mensenkamp 2014, Overbeek 2007, Sheng 2006, Shirts 2018, Simbolo 2015, Spaepen 2006). The variant was also identified in dbSNP (ID: rs63751711) as "With Likely pathogenic, Pathogenic allele", ClinVar (classified as pathogenic by Invitae, GeneDx, Ambry Genetics and six other submitters), Cosmic (3x in skin or Large intestine tissue), UMD-LSDB (15x as causal), Zhejiang University Database (3x), Mismatch Repair Genes Variant Database, and in Insight Hereditary Tumors Database (64x as class 5). The variant was not identified in COGR, or MutDB, databases. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Arg226 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The p.Arg226Gln variant occurs in the last three bases of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. The variant is detected in Exon 8 at donor site of the intron, localized in the splice junction and is predicted to cause abnormal splicing. RNA analysis with a primer localized in exon 8, have shown that this substitution results in a complete loss of exon 8 (Pagenstecher 2006, Sharp 2004, Tournier 2008).  In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. - |
Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Sep 09, 2016 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Mar 15, 2023 | This variant is considered pathogenic. Functional studies indicate this variant impacts protein function [PMID:16341550]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 8571956,16341550]. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jun 22, 2022 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jan 03, 2022 | This variant changes the last nucleotide c.G of exon 8 of the MLH1 gene and is predicted to impair RNA splicing at the intron 8 splice donor site. RNA studies with carrier individuals have shown that this variant cause an out-of-frame skipping of exon 8 (PMID:18561205) and exons 8-10 (PMID: 21034533). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with Lynch syndrome (PMID: 12362047, 12547705, 12624141, 15300854, 16341550, 17453009, 18561205, 21034533). Loss of MLH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.677G>A pathogenic mutation (also known as p.R226Q), located in coding exon 8 of the MLH1 gene, results from a G to A substitution at nucleotide position 677. The amino acid change results in arginine to glutamine at codon 226, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 8, which makes it likely to have some effect on normal mRNA splicing. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This alteration has been reported in numerous hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome families, including individuals whose early-onset tumors demonstrated microsatellite instability, absence of MLH1 and PMS2 on immunohistochemistry, and normal MLH1 methylation levels (Liu SR et al. World J. Gastroenterol. 2004 Sep;10(18):2647-2651; Pigatto F et al. Hered Cancer Clin Pract, 2004 Nov;2:175-84; Overbeek L et al. Br. J. Cancer. 2007 May;96(10):1605-1612; Mueller J et al. Cancer Res, 2009 Sep;69:7053-61; Zhang JX et al. World J Gastroenterol, 2015 Apr;21:4136-49; Goldberg Y et al. Clin Genet, 2015 Jun;87:549-53; Simbolo M et al. Hered Cancer Clin Pract, 2015 Aug;13:18; Carneiro da Silva F et al. PLoS One, 2015 Oct;10:e0139753; Guindalini RS et al. Gastroenterology, 2015 Nov;149:1446-53; Lee J et al. BMC Cancer, 2017 12;17:843; Rohlin A et al. Fam Cancer, 2017 04;16:195-203; Alqahtani M et al. Fam Cancer, 2018 04;17:197-203; Jiang W et al. Int J Cancer, 2019 05;144:2161-2168). In addition, multiple independent RT-PCR studies have demonstrated that this alteration is associated with exon 8 skipping, resulting in a deletion of 89 base pairs that is predicted to cause a translational frameshift (Sharp A et al. Hum. Mutat. 2004 Sep;24(3):272; Pagenstecher C et al. Hum. Genet. 2006 Mar;19(1-2):9-22; Tournier I et al. Hum. Mut. 2008 Dec;29(12):1412-24). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
| Pathogenic, criteria provided, single submitter | curation | Sema4, Sema4 | Jan 15, 2022 | - - |
Lynch syndrome 1 Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | Ding PR Lab, Sun Yat-sen University Cancer Center | - | - - |
Lynch-like syndrome Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | Constitutional Genetics Lab, Leon Berard Cancer Center | Jul 01, 2019 | - - |
Gastric cancer Pathogenic:1
| Pathogenic, no assertion criteria provided | research | Laboratory for Genotyping Development, RIKEN | Jul 01, 2021 | - - |
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 02, 2024 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 226 of the MLH1 protein (p.Arg226Gln). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Lynch syndrome (PMID: 8571956, 12362047, 12547705, 12624141, 15300854, 16341550, 17453009). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 90318). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 8 and introduces a premature termination codon (PMID: 15300854, 16341550, 18561205, 21034533; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. - |
Endometrial carcinoma Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | CZECANCA consortium | Feb 21, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Uncertain
D;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N
REVEL
Pathogenic
Sift
Uncertain
D;D
Sift4G
Benign
T;T
Polyphen
D;.
Vest4
MutPred
Gain of sheet (P = 0.0827);.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -4
DS_DL_spliceai
Position offset: 0
Find out detailed SpliceAI scores and Pangolin per-transcript scores at