chr3-37048955-G-A

Variant names:

• chr3-37048955-G-A
• rs63750217
• NM_000249.4:c.2041G>A

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.2041G>A​(p.Ala681Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). ClinVar reports functional evidence for this variant: "SCV000275301: In vitro studies have shown that while this alteration shows proficient MMR activity, it leads to decreased protein stability and thus, decreased protein expression (Raevaara TE et al. Gastroenterology. 2005 Aug" and additional evidence is available in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A681P) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:26 U:1
• Conservation: PhyloP100: 4.68
• Publications: 71 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: SCV000275301: In vitro studies have shown that while this alteration shows proficient MMR activity, it leads to decreased protein stability and thus, decreased protein expression (Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Takahashi M et al. Cancer Res. 2007 May;67:4595-604; Hinrichsen I et al. Clin. Cancer Res. 2013 May;19:2432-41). Another functional analysis of this variant has demonstrated that this amino acid change causes a reduction in MLH1 and PMS2 binding and a >80% reduction in the interaction between MLH1 and hExo1, a member of a family of conserved exonucleases which are implicated in many DNA metabolic processes, including DNA mismatch repair (MMR) and recombination (Schmutte CJ et al. J. Biol. Chem. 2001 Aug;276:33011-8).; SCV000689855: Functional studies have shown that this variant results in reduced protein expression and stability (PMID: 21404117). This variant has been shown to eliminate the dominant negative mutator effect (PMID: 9697702, 17510385, 21404117) and decrease MMR activity (PMID: 17210669, 17510385).; SCV005901685: "In vitro studies have shown that while this alteration shows proficient MMR activity, it leads to decreased protein stability and thus, decreased protein expression (PMID: 16083711; PMID 17510385; PMID: 23403630, PMID: 31881334)" (PS3_Moderate).; SCV000592438: "In addition, several studies have demonstrated MLH1 immunohistochemistry deficiency or MSI-high tumors in individuals with this deletion (Pedroni_2007, Barnetson_2006, Sheng_2006, Takahashi_2007) increasing the likelihood this variant is pathogenic."; SCV000616784: Published functional studies are discordant: similar in vitro MMR activity compared to wild type, reduced MLH1 expression, reduced binding with PMS2, and significantly reduced binding with MRE11, increased cell survival in a methylation tolerance assay (Guerrette 1999, Vo 2005, Takahashi 2007, Hardt 2011, Drost 2018, Bouvet 2019); SCV000821735: Experimental studies have shown that this missense change disrupts MLH1 protein function (PMID: 9697702, 17510385, 21404117).; SCV004220868: Extensive functional studies indicate this variant has deleterious effects on MLH1 protein expression (PMID 32076465 (2020), 29520894 (2018), 25477341 (2015), 21404117 (2011)), PMS2 binding (PMID 21404117 (2011), 15864295 (2005), 12810663 (2003), 10037723 (1999)), and interactions with MRE11 and EXO1 proteins (PMID 15864295 (2005), 12810663 (2003), 11427529 (2001)).; SCV000218745: Experimental studies have shown that this missense change affects MLH1 function (PMID: 9697702, 10037723, 12810663, 15864295, 16083711, 17510385, 21404117, 25477341).; SCV001519395: multiple functional studies report this variant has an impact on MLH1 protein function and results in reducing interacting with PMS2 and EXO1 proteins, decreasing in vitro MMR activity and MLH1 protein expression (Kondo_2003, Takahashi_2007, Hardt_2011, Koger_2018, PMID: 16083711).
• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 44 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 chr3-37048955-G-C is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 233523.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.96
• PP5: Variant 3-37048955-G-A is Pathogenic according to our data. Variant chr3-37048955-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 17099.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.2041G>A	p.Ala681Thr	missense	Exon 18 of 19	NP_000240.1	P40692-1
	MLH1	NM_001354628.2		c.1948G>A	p.Ala650Thr	missense	Exon 17 of 18	NP_001341557.1	A0A087WX20
	MLH1	NM_001354629.2		c.1942G>A	p.Ala648Thr	missense	Exon 17 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.2041G>A	p.Ala681Thr	missense	Exon 18 of 19	ENSP00000231790.3	P40692-1
	MLH1	ENST00000458205.6	TSL:1	c.1318G>A	p.Ala440Thr	missense	Exon 19 of 20	ENSP00000402667.2	P40692-2
	MLH1	ENST00000456676.7	TSL:1	c.1896+1272G>A		intron	N/A	ENSP00000416687.3	H0Y818

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461836 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727226

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.0000224 AC: 1 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39698

South Asian (SAS) AF: 0.00 AC: 0 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53418

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111962

Other (OTH) AF: 0.00 AC: 0 AN: 60394

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
8	-	-	not provided (8)
6	-	-	Colorectal cancer, hereditary nonpolyposis, type 2 (6)
4	-	-	Hereditary cancer-predisposing syndrome (4)
2	-	-	Lynch syndrome (2)
1	-	-	Hereditary breast ovarian cancer syndrome (1)
1	-	-	Hereditary nonpolyposis colon cancer (1)
1	-	-	Hereditary nonpolyposis colorectal neoplasms (1)
1	-	-	Inherited MMR deficiency (Lynch syndrome) (1)
1	-	-	Muir-Torré syndrome (1)
1	-	-	Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2;C5399763:Mismatch repair cancer syndrome 1 (1)
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.74
BayesDel_addAF	Pathogenic	0.49	D
BayesDel_noAF	Pathogenic	0.47
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.92	D
Eigen	Pathogenic	0.77
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.84	T
M_CAP	Pathogenic	0.42	D
MetaRNN	Pathogenic	0.96	D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.3	M
PhyloP100		4.7
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	-2.2	N
REVEL	Pathogenic	0.83
Sift	Uncertain	0.0030	D
Sift4G	Uncertain	0.0070	D
Polyphen		0.99	D
Vest4		0.87
MutPred		0.82		Gain of phosphorylation at A681 (P = 0.0412)
MVP		0.98
MPC		0.29
ClinPred		0.91	D
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.72
gMVP		0.77
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: rs63750217; hg19: chr3-37090446;