rs63749859

Variant names:

• chr3-37000976-T-C
• rs63749859
• NM_000249.4:c.229T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-37000976-T-C
• chr3-37000976-T-G

Variant summary

Our verdict is Pathogenic. The variant received 22 ACMG points: 22P and 0B. PS3 PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.229T>C​(p.Cys77Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/22 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). ClinVar reports functional evidence for this variant: "SCV000274513: Functional analyses showed that this alteration does not affect dimerization with PMS2; however, an in vitro mismatch repair (MMR) assay indicated that it produces a nonfunctional MLH1 protein (Nystrom-Lahti M et al. Genes Chromosomes Cancer. 2002 Feb;33(2):160-7). In another study involving the same family, additional functional assays showed decreased protein expression, severely deficient MMR activity, and decreased protein subcellular localization (Raevaara TE et al. Gastroenterology. 2005 Aug;129(2):537-49). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD).; SCV001360803: Publications also reported experimental evidence evaluating an impact on protein function, demonstrating preserved interaction with PMS2, but deficient MMR function (Nystrom-Lahti 2002, Raevaara 2005, Borras 2012).; SCV001554150: The MLH1 p.Cys77Arg was shown to decrease MMR activity in multiple functional assays using yeast, increasing the likelihood that it has clinical significance (Ellison 2004, Wanat 2007). Raevaara et al (2005) used site directed mutagenesis to assess non-truncating MLH1 variants for protein expression/stability, subcellular localization, protein-protein interaction and repair efficiency, with the finding that the variant was pathogenic based on deficient MMR activity, decreased protein expression and amino acid conservation. Nystrom-Lahti et al (2002) tested the functionality of this variant with similar findings of MMR deficiency with no effect on hetero-dimerization with PMS2, implying pathogenicity based on nonfunctional protein production.; SCV002149596: Experimental studies have shown that this missense change affects MLH1 function (PMID:11793442, 15475387, 16083711, 17210669, 22736432).". Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C77S) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:5
• Conservation: PhyloP100: 7.56
• Publications: 21 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, Orphanet, G2P
• 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: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, G2P, 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

ACMG classification

Our verdict: Pathogenic. The variant received 22 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV000274513: Functional analyses showed that this alteration does not affect dimerization with PMS2; however, an in vitro mismatch repair (MMR) assay indicated that it produces a nonfunctional MLH1 protein (Nystrom-Lahti M et al. Genes Chromosomes Cancer. 2002 Feb;33(2):160-7). In another study involving the same family, additional functional assays showed decreased protein expression, severely deficient MMR activity, and decreased protein subcellular localization (Raevaara TE et al. Gastroenterology. 2005 Aug;129(2):537-49). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD).; SCV001360803: Publications also reported experimental evidence evaluating an impact on protein function, demonstrating preserved interaction with PMS2, but deficient MMR function (Nystrom-Lahti 2002, Raevaara 2005, Borras 2012).; SCV001554150: The MLH1 p.Cys77Arg was shown to decrease MMR activity in multiple functional assays using yeast, increasing the likelihood that it has clinical significance (Ellison 2004, Wanat 2007). Raevaara et al (2005) used site directed mutagenesis to assess non-truncating MLH1 variants for protein expression/stability, subcellular localization, protein-protein interaction and repair efficiency, with the finding that the variant was pathogenic based on deficient MMR activity, decreased protein expression and amino acid conservation. Nystrom-Lahti et al (2002) tested the functionality of this variant with similar findings of MMR deficiency with no effect on hetero-dimerization with PMS2, implying pathogenicity based on nonfunctional protein production.; SCV002149596: Experimental studies have shown that this missense change affects MLH1 function (PMID: 11793442, 15475387, 16083711, 17210669, 22736432).
• PM1: In a hotspot region, there are 13 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 45 uncertain in NM_000249.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-37000977-G-C is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 422226.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.991
• PP5: Variant 3-37000976-T-C is Pathogenic according to our data. Variant chr3-37000976-T-C is described in ClinVar as Pathogenic. ClinVar VariationId is 90110.Status of the report is reviewed_by_expert_panel, 3 stars.

Variant Effect in Transcripts

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

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	NM_000249.4	MANE Select	c.229T>C	p.Cys77Arg	missense	Exon 3 of 19	NP_000240.1	P40692-1
	MLH1	NM_001354628.2		c.229T>C	p.Cys77Arg	missense	Exon 3 of 18	NP_001341557.1	A0A087WX20
	MLH1	NM_001354630.2		c.229T>C	p.Cys77Arg	missense	Exon 3 of 18	NP_001341559.1	A0A669KAW3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	ENST00000231790.8	TSL:1 MANE Select	c.229T>C	p.Cys77Arg	missense	Exon 3 of 19	ENSP00000231790.3	P40692-1
	MLH1	ENST00000456676.7	TSL:1	c.229T>C	p.Cys77Arg	missense	Exon 3 of 17	ENSP00000416687.3	H0Y818
	MLH1	ENST00000413740.2	TSL:1	c.229T>C	p.Cys77Arg	missense	Exon 3 of 15	ENSP00000416476.2	H0Y806

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

Alfa AF: 0.000129 Hom.: 0

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
1	-	-	Hereditary cancer-predisposing syndrome (1)
1	-	-	Hereditary nonpolyposis colon cancer (1)
1	-	-	Hereditary nonpolyposis colorectal neoplasms (1)
1	-	-	Lynch syndrome (1)
1	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.55	D
BayesDel_noAF	Pathogenic	0.56
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D
Eigen	Pathogenic	0.98
Eigen_PC	Pathogenic	0.91
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.98	D
M_CAP	Pathogenic	0.31	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.9	H
PhyloP100		7.6
PrimateAI	Pathogenic	0.88	D
PROVEAN	Pathogenic	-10	D
REVEL	Pathogenic	0.96
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.96
MutPred		0.96		Gain of disorder (P = 0.0348)
MVP		0.98
MPC		0.53
ClinPred		1.0	D
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		1.0
gMVP		0.96
Mutation Taster		=1/99	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs63749859; hg19: chr3-37042467;