3-37017508-C-T

Variant names:

• chr3-37017508-C-T
• rs63751194
• NM_000249.4:c.793C>T
• MLH1 p.Arg265Cys

GermlineCancer (beta)

Variant summary

Our verdict is Pathogenic.

>+14 Pathogenic

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 22 classification points (ACMG Germline Pathogenicity v2019). PS3PM1PM2PM5PP3_StrongPP5_Very_Strong

The NM_000249.4(MLH1):c.793C>T (p.Arg265Cys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a cumulative frequency of 0.000000684 (AC=1) in the gnomAD database across 1,461,428 control chromosomes (no homozygotes observed). The grpmax filtering allele frequency (95% CI) is 0.0000009. In-silico predictor (REVEL) classifies this variant as likely damaging/oncogenic. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. The affected nucleotide is highly conserved across species (PhyloP 100-way vertebrate score: 7.28). Variant has been reported in ClinVar as Pathogenic/Likely Pathogenic (★★★). ClinVar reports functional evidence for this variant: "SCV004176523: Functional studies demonstrate skipping of exon 9-10, aberrant splicing, reduced mRNA and protein expression as well as deceased protein stability, hence proving a damaging effect (Fan Y, et. al., 2012" and additional evidence is available in ClinVar. A different missense at the same amino acid position has been reported as Pathogenic/Likely Pathogenic in ClinVar: p.R265V: Pathogenic (ClinVar VariationId 619508, 1 star) Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.R265H: Conflicting_classifications_of_pathogenicity (ClinVar VariationId 90381); p.R265L: Uncertain_significance (ClinVar VariationId 1928288, 2 stars); p.R265= (synonymous): Likely_benign (ClinVar VariationId 491730, 2 stars) This exact variant is established as oncogenic in: CGI (Cancer Genome Interpreter). This exact variant is curated in the UniProt human variants database as Uncertain Significance, associated with Colorectal cancer, hereditary nonpolyposis, type 2 (hnpcc2); it is also listed as a COSMIC curated somatic variant.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: MLH1 NM_000249.4 missense, splice_region
• Clinical Significance: Pathogenic reviewed by expert panel P:24 U:1 O:1
• Conservation: PhyloP100: 7.28
• Publications: 1 publications found

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: ClinGen, G2P, Orphanet
• Lynch syndrome 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Ambry Genetics
• Muir-Torre syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, G2P, Ambry Genetics
• mismatch repair cancer syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• 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

Classification according to ACMG Germline Pathogenicity v2019

Specifications for MLH1 are available in the ClinGen Criteria Specification Registry and recommended for reference when assigning criteria.

Classification was made for transcript:

Our verdict: Pathogenic. The variant received 22 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PS3Functional studies show damaging effect		Well-established functional study supports damaging effect (PS3); SCV004176523: Functional studies demonstrate skipping of exon 9-10, aberrant splicing, reduced mRNA and protein expression as well as deceased protein stability, hence proving a damaging effect (Fan Y, et. al., 2012; Casey G, et. al., 2005).; SCV000279078: Published functional studies demonstrate a damaging effect: aberrant splicing and reduced mRNA and protein expression as well as deceased protein stability and reduced binding of MLH1 to PMS2 (PMID: 12386821, 15713769, 18205192, 20864636, 22753075, 21952876, 26761715).; SCV005623591: Functional studies suggest reduced expression, protein stability, and mismatch repair activity of the variant protein (PMIDs: 17510385 (2007), 17135187 (2006), and 11555625 (2001)).; SCV005877790: "In vitro functional analyses demonstrate an effect on splicing at the transcript level (van der Klift 2014) and a loss of mismatch repair activity at the protein level (Drost 2010)."; SCV000696181: Functional studies report the variant to result in exon skipping and a partial MMR defect which in combination likely result in a pathogenic impact.; SCV000731294: Functional studies using patient mRNA showed that the variant leads to exon skipping and protein truncation (Casey 2005).; SCV000276047: This mutation has been associated with exon-skipping, premature protein truncation, and low expression of the variant allele (Casey G et al. JAMA. 2005 Feb;293:799-809; Tournier I et al. Hum. Mut. 2008 Dec;29:1412-24; van der Klift HM et al. Mol. Genet. Genomic Med. 2015 Jul;3:327-45).; SCV000684870: Functional studies have shown that this variant significantly decreases MLH1 protein stability (PMID: 18205192) and the ability of MLH1 protein to bind PMS2 (PMID: 21952876).; SCV000262499: Studies have shown that this missense change alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 18561205, 22736432, 26247049; Invitae).; SCV000592378: This variant has been tested in different functional assays at the protein level, with results that were not always consistent; the p.Arg265Cys was associated with a mild reduction of mismatch repair efficiency in four studies (Plotz 2006; Ellison 2001; Wanat 2007; Takahashi 2007) but not in a fifth one (Trojan 2002) (Tournier 2007).
	PM1Mutational hot spot or critical domain		Missense neighbourhood hotspot (≥2 P/LP within ±8 AA, OR ≥ 5 vs. background) — PM1; In-domain: 0 pathogenic, 0 benign rare missense variants.; ±8 AA neighbourhood: 4 pathogenic, 3 benign (OR vs. background: 6.4).
	PM2Absent/extremely low in population databases		Very rare in gnomAD for AD/XL gene (popmax AF < threshold/10) — PM2; GnomAD popmax AF = 0.0000009 — very rare for AD+AR gene (base 0.0001, raised to 0.0005 by highest known P/LP ClinVar AF 0.000636) — PM2 moderate.
	PM5Novel missense at known pathogenic residue		Different pathogenic missense at same AA residue in ClinVar (PM5); ClinVar contains a germline Pathogenic/Likely Pathogenic entry at the same amino acid position with a different amino acid change: p.R265V: Pathogenic (ClinVar VariationId 619508, 1 star); Other variants at the same amino acid residue (not pathogenic): p.R265H: Conflicting_classifications_of_pathogenicity (ClinVar VariationId 90381); p.R265L: Uncertain_significance (ClinVar VariationId 1928288, 2 stars); p.R265= (synonymous): Likely_benign (ClinVar VariationId 491730, 2 stars)
	PP3Computational evidence supports damaging effect		Germline meta computational scorer (REVEL/MetaRNN/BayesDel) predicts damaging effect — strong evidence (PP3); Splicing verdict: not pathogenic.; Germline computational verdict: pathogenic (Strong).
	PP5Reputable source reports pathogenic		ClinVar ≥3 stars pathogenic — very strong (PP5); ClinVar submissions overwhelmingly pathogenic (≥10 total, ≥80% P/LP, <10% B/LB) — strong (PP5, count-based); ClinVar germline classification: Pathogenic/Likely Pathogenic, 3 star(s). ClinVar submissions strongly and reliably favor pathogenicity (24/25 total P/LP).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_000249.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	MLH1 NM_000249.4	MANE Select	c.793C>T p.Arg265Cys	missensesplice_region	Exon 10 of 19	Prot: NP_000240.1 UniProt:
	MLH1 NM_001354628.2		c.793C>T p.Arg265Cys	missensesplice_region	Exon 10 of 18	Prot: NP_001341557.1 UniProt:
	MLH1 NM_001354629.2		c.694C>T p.Arg232Cys	missensesplice_region	Exon 9 of 18	Prot: NP_001341558.1 UniProt:

MLH1 NM_000249.4

MANE Select

HGVSc / HGVSpc.793C>Tp.Arg265Cys

Exon rankExon 10 of 19

missensesplice_region

Prot: NP_000240.1UniProt: P40692-1

MLH1 NM_001354628.2

HGVSc / HGVSpc.793C>Tp.Arg265Cys

Exon rankExon 10 of 18

missensesplice_region

Prot: NP_001341557.1UniProt: A0A087WX20

MLH1 NM_001354629.2

HGVSc / HGVSpc.694C>Tp.Arg232Cys

Exon rankExon 9 of 18

missensesplice_region

Prot: NP_001341558.1UniProt: A0AAQ5BGZ2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	MLH1 ENST00000231790.8	TSL:1MANE Select	c.793C>T p.Arg265Cys	missensesplice_region	Exon 10 of 19	Prot: ENSP00000231790.3 UniProt:
	MLH1 ENST00000456676.7	TSL:1	c.793C>T p.Arg265Cys	missensesplice_region	Exon 10 of 17	Prot: ENSP00000416687.3 UniProt:
	MLH1 ENST00000413740.2	TSL:1	c.793C>T p.Arg265Cys	missensesplice_region	Exon 10 of 15	Prot: ENSP00000416476.2 UniProt:

MLH1 ENST00000231790.8

TSL:1MANE Select

HGVSc / HGVSpc.793C>Tp.Arg265Cys

Exon rankExon 10 of 19

missensesplice_region

Prot: ENSP00000231790.3UniProt: P40692-1

MLH1 ENST00000456676.7

TSL:1

HGVSc / HGVSpc.793C>Tp.Arg265Cys

Exon rankExon 10 of 17

missensesplice_region

Prot: ENSP00000416687.3UniProt: H0Y818

MLH1 ENST00000413740.2

TSL:1

HGVSc / HGVSpc.793C>Tp.Arg265Cys

Exon rankExon 10 of 15

missensesplice_region

Prot: ENSP00000416476.2UniProt: H0Y806

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 5 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF: 6.84e-7	AC:1	Hom:0	AN:1461428	Cov:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32
TOPMed (Bravo)	AF: 0.00000378	AC:1	Hom:0	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.0000175	AC:1	Hom:0	AN:57126	Cov:

Showing 5 sources

Case/control cohorts

Cohort	Cases			Controls
	AF	AC	AN	AF	AC	AN
Epi25(Epilepsy)	0.0000238	1	41956	0.00	0	66876
SCHEMA(Schizophrenia)	0.00	0	48008	0.0000135	1	73916

Showing 2 cohortsAllele count / allele number. AF is computed from the counts for ASC (not provided by the source).

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
7	1	-	not provided (8)
6	-	-	Colorectal cancer, hereditary nonpolyposis, type 2 (6)
3	-	-	Lynch syndrome (3)
2	-	-	Carcinoma of colon (2)
2	-	-	Hereditary cancer-predisposing syndrome (2)
1	-	-	Hereditary nonpolyposis colon cancer (1)
1	-	-	Hereditary nonpolyposis colorectal neoplasms (1)
1	-	-	Lynch syndrome 1 (2)
1	-	-	Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2;C5399763:Mismatch repair cancer syndrome 1 (1)

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	35
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.59
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.90	D
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	1.0	D
FuncVEP CTI	Pathogenic	1.0
GPN-Star LLR	N/A	-8.5
GPN-Star score	N/A	8.5
LIST_S2	Pathogenic	0.99	D
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	0.94	D
Mutation Taster	N/A	0/100	disease causing (ClinVar)
MutationAssessor	Pathogenic	4.8	H
PhyloP100	Uncertain	7.3
popEVE	Benign	-4.0
PrimateAI	Uncertain	0.72	T
PROVEAN	Pathogenic	-7.8	D
RBP_binding_hub_radar	N/A	0.0
RBP_regulation_power_radar	N/A	1.7
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Varity_R	N/A	0.96
VESM-3B	Benign	-12

Showing 30 of 30 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Uncertain	0.34
Pangolin loss	Uncertain	0.34	Position offset: -2
SpliceAI score (max)	Benign	0.15	Details are displayed if max score is > 0.2

Showing 3 of 3 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs63751194;

hg19: chr3-37058999;

COSMIC: COSV51616044;

COSMIC: COSV51616044;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar