ENST00000458205.6:c.-422G>T

Variant names:

• chr3-37001049-G-T
• rs267607727
• ENST00000458205.6:c.-422G>T

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PM2 PP3_Strong PP5

The ENST00000458205.6(MLH1):​c.-422G>T variant causes a 5 prime UTR premature start codon gain 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. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 ENST00000458205.6 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1
• Conservation: PhyloP100: 9.42
• Publications: 7 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: G2P, ClinGen, Orphanet
• 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: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet, 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: Likely_pathogenic. The variant received 7 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: REVEL computational evidence supports a deleterious effect, 0.96
• PP5: Variant 3-37001049-G-T is Pathogenic according to our data. Variant chr3-37001049-G-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 1723354.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458205.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	NM_000249.4	MANE Select	c.302G>T	p.Gly101Val	missense	Exon 3 of 19	NP_000240.1
	MLH1	NM_001167618.3		c.-422G>T		5_prime_UTR_premature_start_codon_gain	Exon 3 of 19	NP_001161090.1
	MLH1	NM_001167619.3		c.-330G>T		5_prime_UTR_premature_start_codon_gain	Exon 3 of 18	NP_001161091.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	ENST00000458205.6	TSL:1	c.-422G>T		5_prime_UTR_premature_start_codon_gain	Exon 4 of 20	ENSP00000402667.2
	MLH1	ENST00000231790.8	TSL:1 MANE Select	c.302G>T	p.Gly101Val	missense	Exon 3 of 19	ENSP00000231790.3
	MLH1	ENST00000456676.7	TSL:1	c.302G>T	p.Gly101Val	missense	Exon 3 of 17	ENSP00000416687.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1

Feb 16, 2022

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.G101V variant (also known as c.302G>T), located in coding exon 3 of the MLH1 gene, results from a G to T substitution at nucleotide position 302. The glycine at codon 101 is replaced by valine, an amino acid with dissimilar properties. This alteration has been observed in an individual whose colorectal tumor demonstrated high microsatellite instability and family history was consistent with Lynch syndrome (Hardt K et al. Fam. Cancer, 2011 Jun;10:273-84). This alteration demonstrated disrupted interaction with PMS2 and an intermediate dominant negative effect in yeast two hybrid assays (Hardt K et al. Fam. Cancer, 2011 Jun;10:273-84). Based on internal structural analysis using published crystal structures, this alteration is anticipated to result in a significant decrease in structural stability (Wu H et al. Acta Crystallogr F Struct Biol Commun, 2015 Aug;71:981-5). Another alteration at the same codon, p.G101D (c.302G>A), has been identified in a family meeting Bethesda guidelines (Taylor CF et al. Hum. Mutat. 2003 Dec; 22(6):428-33), and two in vitro functional studies demonstrated reduced MMR function and decreased expression for p.G101D when compared to wild-type MLH1 in yeast (Ellison AR et al. Nucleic Acids Res. 2004 ; 32(18):5321-38; Hinrichsen I et al. Clin. Cancer Res. 2013 May; 19(9):2432-41). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

not specified Uncertain:1

Oct 03, 2022

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: MLH1 c.302G>T (p.Gly101Val) results in a non-conservative amino acid change located in the DNA mismatch repair protein family, N-terminal (IPR002099) of the encoded protein sequence. Five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251344 control chromosomes. c.302G>T has been reported in the literature in an individual affected with Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome (example, Hardt_2011). At least one publication reports experimental evidence suggesting reduced interaction of MLH1 with PMS2, possibly interfering with MMR efficiency (Hardt_2011). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.62
CADD	Pathogenic	34
DANN	Uncertain	0.99
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.88
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Uncertain	0.22	D
PhyloP100		9.4
ClinPred		1.0	D
GERP RS		5.9
Varity_R		1.0
Mutation Taster		=5/95	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
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: rs267607727; hg19: chr3-37042540; COSMIC: COSV99212305;