rs587779001

Variant names:

• chr3-36993521-C-A
• rs587779001
• NM_000249.4:c.-27C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-36993521-C-A
• chr3-36993521-C-G
• chr3-36993521-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2 PP5_Very_Strong BP4

The NM_000249.4(MLH1):​c.-27C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MLH1 NM_000249.4 5_prime_UTR
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8
• Conservation: PhyloP100: -0.314

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-36993521-C-A is Pathogenic according to our data. Variant chr3-36993521-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 89589.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-36993521-C-A is described in Lovd as [Pathogenic]. Variant chr3-36993521-C-A is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.-27C>A		5_prime_UTR_variant	Exon 1 of 19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790	c.-27C>A		5_prime_UTR_variant	Exon 1 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1457220 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 725246

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:2

Sep 26, 2017

Counsyl

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 06, 2023

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 21840485, 22878509]. -

not provided Pathogenic:2

Jun 03, 2020

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MLH1 c.-27C>A has been reported in cis with MLH1 c.85G>T (p.Ala29Ser) in patients with Lynch-related cancers and tumor studies consistent with pathogenic variants in this gene (Raevaara 2005, Hitchins 2011, Ward 2013, Kwok 2014); Published functional studies demonstrate that while MLH1 c.-27C>A does not appear to affect the start codon or Kozak translation consensus sequence, it results in significantly reduced promoter activity while the MLH1 c.[-27C>A;85G>T] haplotype results in constitutional MLH1 promoter methylation and reduced allelic expression (Hitchins 2011, Kwok 2014); Not observed in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 26888055, 22878509, 16083711, 21840485, 24084575, 25910213, 17301300, 23462881, 29472279, 27435373) -

Oct 10, 2022

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Functional studies have reported that this variant results in a deleterious effect on MLH1 promoter activity (PMID: 21840485 (2011)). The MLH1 c.-27C>A variant is commonly found in cis with the MLH1 c.85G>T (p.Ala29Ser) variant. The MLH1 c.-27C>A and c.85G>T (p.Ala29Ser) haplotype has been reported in multiple individuals with colorectal cancer or a Lynch Syndrome associated phenotype (PMID: 27435373 (2016), 26888055 (2016), 24084575 (2014), 22878509 (2013), 21840485 (2011), 21120944 (2011)) and has been shown to cause MLH1 promoter methylation and affect allelic expression (PMID: 22878509 (2013), 21840485 (2011)). Based on the available information, this MLH1 c.-27C>A variant is classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Feb 18, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

****************HAPTOTYPE RD************************ The c.-27C>A alteration is located in the 5' untranslated region (5’UTR) of the MLH1 gene. This variant results from a C to A substitution 27 nucleotides upstream from the first translated codon. The p.A29S alteration (also known as c.85G>T) is located in coding exon 1 of the MLH1 gene. This alteration results from a G to T substitution at nucleotide position 85. The alanine at codon 29 is replaced by serine, an amino acid with similar properties. The c.-27C>A and c.85G>T alterations are linked in cis, as both are part of a European ancestral haplotype. The c.[-27C>A;85G>T] haplotype has been reported to be linked to a constitutional MLH1 epimutation in several unrelated families that either met Amsterdam I/II criteria or were suspected to have HNPCC/Lynch syndrome (Kwok CT et al. Eur. J. Hum. Genet. 2014 May;22(5):617-24; Hitchins MP et al. Cancer Cell 2011;20:200-13; Ward RL et al. Genet. Med. 2013;15:25-35). Within these families, the c.[-27C>A;85G>T] haplotype was associated with differing levels of MLH1 promoter constitutional methylation and with loss of PMS2 and/or MLH1 staining on immunohistochemistry in tumor samples (Kwok CT et al. Eur. J. Hum. Genet. 2014 May;22(5):617-24; Hitchins MP et al. Cancer Cell 2011;20:200-13; Ward RL et al. Genet. Med. 2013;15:25-35). Luciferase reporter assays performed for the c.-27C>A alteration demonstrated reduced promoter activity (Hitchins MP et al. Cancer Cell 2011;20:200-13; Ward RL et al. Genet. Med. 2013;15:25-35). In contrast, luciferase reporter assays performed for the c.85G>T alteration showed little to no reduction in promoter activity compared to wild type suggesting the c.-27C>A alteration accounts for allelic repression of MLH1 transcription resulting in loss of MLH1 expression; however, a direct causal relationship has yet to be clarified (Hitchins MP et al. Cancer Cell 2011;20:200-13). Based on the supporting evidence, the c.[-27C>A;85G>T] haplotype is interpreted as a disease-causing mutation. ************************c.-27C>A alone RD**************************(use only when p.A29S is not identified with c.-27C>A)*************** The c.-27C>A alteration is located in the 5' untranslated region (5’UTR) of the MLH1 gene. This variant results from a C to A substitution 27 nucleotides upstream from the first translated codon. This alteration has been reported in multiple unrelated HNPCC/Lynch syndrome families as part of a haplotype in conjunction with MLH1 p.A29S (Kwok CT et al, Eur. J. Hum. Genet. 2014 May;22(5):617-24; Hitchins MP et al. Cancer Cell 2011;20:200-13; Ward RL et al. Genet. Med. 2013;15:25-35). Within these families, the c.-27C>A + p.A29S haplotype was associated with loss of MLH1 and PMS2 staining in tumor samples and inconsistent levels of MLH1 promoter methylation/transcriptional silencing in normal tissues. However, luciferase reporter assays performed by Hitchins and colleagues suggest that the c.-27C>A alteration, and not p.A29S, reduced MLH1 promoter activity significantly and that retention of cytosine at position -27 is crucial for optimal MLH1 transcription in somatic cells. Based on the available evidence, this alteration is classified as pathogenic. -

Jul 14, 2021

Sema4, Sema4

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

- -

not specified Pathogenic:1

Jan 07, 2022

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Jun 21, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant occurs in a non-coding region of the MLH1 gene. It does not change the encoded amino acid sequence of the MLH1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with Lynch syndrome (PMID: 16083711, 21840485, 22878509, 24084575). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 89589). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects MLH1 function (PMID: 21840485, 22878509). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.7
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs587779001; hg19: chr3-37035012;