2-47408415-C-T

Position:

• chr2-47408415-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000251.3(MSH2):​c.226C>T​(p.Gln76*) variant causes a stop gained change. 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 Pathogenic (★★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 31)
• Consequence: MSH2 NM_000251.3 stop_gained
• Clinical Significance: Pathogenic reviewed by expert panel P:8
• Conservation: PhyloP100: 6.59

Genes affected

MSH2 (HGNC:7325): (mutS homolog 2) This locus is frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). When cloned, it was discovered to be a human homolog of the E. coli mismatch repair gene mutS, consistent with the characteristic alterations in microsatellite sequences (RER+ phenotype) found in HNPCC. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-47408415-C-T is Pathogenic according to our data. Variant chr2-47408415-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 90945.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47408415-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSH2	NM_000251.3	c.226C>T	p.Gln76*	stop_gained	2/16	ENST00000233146.7	NP_000242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSH2	ENST00000233146.7	c.226C>T	p.Gln76*	stop_gained	2/16	1	NM_000251.3	ENSP00000233146.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: reviewed by expert panel

Submissions by phenotype

Lynch syndrome 1 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jul 26, 2023	This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. -
Pathogenic, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 10, 2023	The substitution creates a nonsense variant, which changes a Glutamine to a premature stop codon, and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been reported in several individuals with Lynch syndrome (Stormorken 2005, Sjursen 2010, Bonnet 2012). MSH2 Gln76Ter was also observed in multiple members of a large Kuwaiti family meeting Amsterdam Criteria; three members of this family presented in childhood with lymphoma, and two of these children were confirmed to be homozygous for this variant (Scott 2007, Marafie 2009). This variant is considered pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 12, 2018	This variant is denoted MSH2 c.226C>T at the cDNA level and p.Gln76Ter (Q76X) at the protein level. The substitution creates a nonsense variant, which changes a Glutamine to a premature stop codon (CAG>TAG), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been reported in several individuals meeting Amsterdam II Criteria or Bethesda Guidelines for Lynch syndrome (Stormorken 2005, Sjursen 2010, Bonnet 2012). MSH2 Gln76Ter was also observed in multiple members of a large Kuwaiti family meeting Amsterdam Criteria; three members of this family presented in childhood with lymphoma and café-au-lait macules, and two of these children were confirmed to be homozygous for this variant (Scott 2007, Marafie 2009). Results from several functional assays in cells homozygous for MSH2 Gln76Ter were consistent with observations from MSH2 knockout mice, which have demonstrated reduced RAD51 loci and increased chromosome damage after ionizing radiation (Barwell 2007). This variant is considered pathogenic. -
Pathogenic, no assertion criteria provided	research	Mayo Clinic Laboratories, Mayo Clinic	-	- -

Lynch-like syndrome Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Constitutional Genetics Lab, Leon Berard Cancer Center

Jul 01, 2019

- -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Coding sequence variation introducing premature termination codon -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 08, 2023

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 90945). This premature translational stop signal has been observed in individual(s) with Lynch syndrome and/or mediastinal T-cell non-Hodgkin lymphoma (PMID: 16034045, 17601929, 19669601, 20587412, 22480969, 28874130). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln76*) in the MSH2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 24362816). -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 11, 2022

The p.Q76* pathogenic mutation (also known as c.226C>T), located in coding exon 2 of the MSH2 gene, results from a C to T substitution at nucleotide position 226. This changes the amino acid from a glutamine to a stop codon within coding exon 2. This alteration has been reported in a patient diagnosed with colorectal cancer at age 59 whose tumor showed absent staining for the MSH2 protein via immunohistochemistry (Stormorken A et al. J. Clin. Oncol. 2005 Jul;23(21):4705-12). It has also been reported in two large and highly consanguineous families in Kuwait who meet Amsterdam criteria (Marafie MJ et al. Fam. Cancer 2009;8(4):289-98). In one of these families, three siblings who were homozygous for this alteration developed non-Hodgkin lymphoma and pigmentary skin abnormalities in early childhood, consistent with a diagnosis of constitutional mismatch repair-deficiency (CMMR-D) syndrome; their parents, who were first cousins, were presymptomatic heterozygous carriers of this alteration (Scott RH et al. J. Med. Genet. 2007 Jul;44(7):e83). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.63
CADD	Pathogenic	40
DANN	Uncertain	1.0
Eigen	Pathogenic	0.85
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Uncertain	0.91	D
Vest4		0.80
GERP RS		4.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs63750042; hg19: chr2-47635554; COSMIC: COSV99252931;