NM_000249.4:c.199G>A

Variant names:

• chr3-36996701-G-A
• rs63750206
• NM_000249.4:c.199G>A

Variant summary

Our verdict is Pathogenic. The variant received 30 ACMG points: 30P and 0B. PS1_Very_Strong PS3 PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.199G>A​(p.Gly67Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,462 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 14/22 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: "SCV000711428: Mice carrying the p.Gly67Arg variant have a strong cancer predisposition phenotype (Avdievich 2008)." and additional evidence is available in ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely pathogenic in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G67V) has been classified as Likely pathogenic. The gene MLH1 is included in the ClinGen Criteria Specification Registry.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:24 U:1
• Conservation: PhyloP100: 9.51
• Publications: 82 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

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

Our verdict: Pathogenic. The variant received 30 ACMG points.

• PS1: Transcript NM_000249.4 (MLH1) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar.
• PS3: PS3 evidence extracted from ClinVar submissions: SCV000711428: Mice carrying the p.Gly67Arg variant have a strong cancer predisposition phenotype (Avdievich 2008).; SCV000172728: "In addition, functional studies have demonstrated that this variant results in low (5.9%) in vitro mismatch repair activity and decreased (<25%) relative MLH1 expression, and demonstrated no dominant mutator effect in reporter assays in yeast, which is consistent with pathogenicity (Takahashi M et al. Cancer Res. 2007 May;67(10):4595-604; Shimodaira H et al. Nat Genet, 1998 Aug;19:384-9; Shcherbakova PV et al. Mol Cell Biol 1999 Apr;19(4):3177-83)."; SCV000821734: Furthermore, functional and in silico analysis (PMID: 17510385, PMID: 17510385) have indicated that this mutation is responsible of Lynch Syndrome occurrence in carriers.; SCV000911366: Functional studies have shown that this variant causes a significant reduction in protein expression and DNA mismatch repair activity (PMID: 24362816) and that mice transgenic for the mutant gene develop tumors and show a severely reduced survival rate (PMID: 18337503).; SCV006324712: Multiple experimental studies have shown that this variant affects MLH1 protein function and stability, showing a functional Odds for Pathogenicity > 18.7 in a calibrated CIMRA assay (PMIDs: 30504929, 30998989, 17510385, 22736432, 12810663, 16982745, 16083711, 22753075, 31494577, among others) (PS3).; SCV000211109: Published functional studies demonstrate a damaging effect: loss of dominant mutator effect, deficient nuclear localization, reduced protein expression, increased mutation rate, and defective mismatch repair activity (PMID: 9697702, 10082584, 11555625, 16083711, 16982745, 17510385, 18337503, 20020535, 21120944, 22753075, 22736432, 36054288); SCV004220863: "In published functional studies, this variant was demonstrated to have a damaging effect on MLH1 function and cause defective mismatch repair activity" (PMIDs: 18337503 (2008), 18094436 (2007), 16083711 (2005), 12810663 (2003), 9697702 (1998), 32849802(2020), 30504929 (2018)).; SCV000253789: Experimental studies have shown that this missense change affects MLH1 function (PMID: 9697702, 11555625, 12810663, 16083711, 18094436, 18337503, 22949379).; SCV004190024: Functional studies indicate this variant impacts protein function [PMID: 16083711, 16982745, 20020535, 22736432].; SCV001478775: Experimental evidence demonstrated that variant had no impact on splicing (e.g. Auclair_2006), and the variant protein had normal interaction with PMS2, however it had decreased expression, impaired subcellular localization, and decreased repair activity compared to wild type (e.g. Raevaara_2005, Andersen_2012, Drost_2019).; SCV000592337: Functional studies have shown that compared to the wild-type protein, the p.Gly67Arg variant showed a severe reduction in repair capacity, and mice studies showed that the variant affected protein stability and led to a strong cancer predisposition phenotype (Blasi 2006, Shimodaira 1998, Clyne 2009, Avdievich 2008).
• PM1: In a hotspot region, there are 15 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 40 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 chr3-36996702-G-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 800484.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.977
• PP5: Variant 3-36996701-G-A is Pathogenic according to our data. Variant chr3-36996701-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 89992.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.199G>A	p.Gly67Arg	missense	Exon 2 of 19	NP_000240.1	P40692-1
	MLH1	NM_001354628.2		c.199G>A	p.Gly67Arg	missense	Exon 2 of 18	NP_001341557.1	A0A087WX20
	MLH1	NM_001354629.2		c.199G>A	p.Gly67Arg	missense	Exon 2 of 18	NP_001341558.1	A0AAQ5BGZ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	ENST00000231790.8	TSL:1 MANE Select	c.199G>A	p.Gly67Arg	missense	Exon 2 of 19	ENSP00000231790.3	P40692-1
	MLH1	ENST00000456676.7	TSL:1	c.199G>A	p.Gly67Arg	missense	Exon 2 of 17	ENSP00000416687.3	H0Y818
	MLH1	ENST00000413740.2	TSL:1	c.199G>A	p.Gly67Arg	missense	Exon 2 of 15	ENSP00000416476.2	H0Y806

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1459462 Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2 AN XY: 726230

African (AFR) AF: 0.00 AC: 0 AN: 33426

American (AMR) AF: 0.00 AC: 0 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26128

East Asian (EAS) AF: 0.00 AC: 0 AN: 39676

South Asian (SAS) AF: 0.00 AC: 0 AN: 86200

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53398

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5762

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1109848

Other (OTH) AF: 0.00 AC: 0 AN: 60306

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
7	-	-	not provided (7)
5	1	-	Colorectal cancer, hereditary nonpolyposis, type 2 (6)
4	-	-	Hereditary cancer-predisposing syndrome (4)
3	-	-	Lynch syndrome (3)
1	-	-	Carcinoma of colon (1)
1	-	-	Hereditary nonpolyposis colon cancer (1)
1	-	-	Hereditary nonpolyposis colorectal neoplasms (1)
1	-	-	Lynch syndrome 1 (1)
1	-	-	Lynch-like syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.62
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.97	D
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.1
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	1.0	D
M_CAP	Pathogenic	0.60	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	0.90	D
MutationAssessor	Pathogenic	5.0	H
PhyloP100		9.5
PrimateAI	Pathogenic	0.82	D
PROVEAN	Pathogenic	-7.3	D
REVEL	Pathogenic	0.99
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.98
MutPred		1.0		Gain of MoRF binding (P = 0.089)
MVP		0.99
MPC		0.44
ClinPred		1.0	D
GERP RS		5.8
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.6
Varity_R		0.98
gMVP		0.95
Mutation Taster		=156/144	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: rs63750206; hg19: chr3-37038192; COSMIC: COSV51614574; COSMIC: COSV51614574;