rs63750474
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Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_000251.3(MSH2):c.1700_1704del(p.Lys567ArgfsTer3) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000421 in 1,423,666 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
MSH2
NM_000251.3 frameshift
NM_000251.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.46
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 2-47471001-TAAAAC-T is Pathogenic according to our data. Variant chr2-47471001-TAAAAC-T is described in ClinVar as [Pathogenic]. Clinvar id is 90755.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47471001-TAAAAC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSH2 | NM_000251.3 | c.1700_1704del | p.Lys567ArgfsTer3 | frameshift_variant | 11/16 | ENST00000233146.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSH2 | ENST00000233146.7 | c.1700_1704del | p.Lys567ArgfsTer3 | frameshift_variant | 11/16 | 1 | NM_000251.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000421 AC: 6AN: 1423666Hom.: 0 AF XY: 0.00000422 AC XY: 3AN XY: 710894
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
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Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:5
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Lynch syndrome 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Aug 03, 2023 | This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. - |
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 - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 16, 2015 | This deletion of 5 nucleotides in MSH2 is denoted c.1700_1704delAAACA at the cDNA level and p.Lys567ArgfsX3 (K567RfsX3) at the protein level. The normal sequence, with the bases that are deleted in brackets, is AATA[AAACA]GAAT. The deletion causes a frameshift, which changes a Lysine to an Arginine at codon 567, and creates a premature stop codon at position 3 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. MSH2 Lys567ArgfsX3 has been observed in at least one family presenting with the Muir-Torre variant of Lynch syndrome (Kruse 1996, Mangold 2004). we consider this variant to be pathogenic. - |
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2023 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 90755). This variant is also known as 1699delAAACA and 1700-4del. This premature translational stop signal has been observed in individual(s) with Lynch syndrome or Muir-Torre syndrome (PMID: 8931714, 11208710, 11606497). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys567Argfs*3) 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 | Apr 12, 2024 | The c.1700_1704delAAACA pathogenic mutation, located in coding exon 11 of the MSH2 gene, results from a deletion of 5 nucleotides at nucleotide positions 1700 to 1704, causing a translational frameshift with a predicted alternate stop codon (p.K567Rfs*3). This mutation has been reported in multiple individuals diagnosed with MSH2-deficient and/or microsatellite unstable colorectal cancer (Terdiman et al. Gastroenterology. 2001 Jan;120(1):21-30; Samowitz WS et al. Gastroenterology. 2001 Oct;121:830-8; Ambry internal data), as well as in an individual diagnosed with Muir-Torre syndrome (Mangold E et al. J Med Genet. 2004 Jul;41(7):567-72). Of note, this mutation is also designated as 1699del5 and 1700-4del in published literature. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at