ClinVar Miner

Submissions for variant NM_002439.5(MSH3):c.178G>C (p.Ala60Pro) (rs2001675)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV001013164 SCV001173712 benign Hereditary cancer-predisposing syndrome 2018-09-17 criteria provided, single submitter clinical testing General population or sub-population frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Genome Sciences Centre, British Columbia Cancer Agency RCV000786036 SCV000924577 uncertain significance Cavernous sinus meningioma 2019-05-21 no assertion criteria provided research
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357722 SCV001553275 likely benign not provided no assertion criteria provided clinical testing The MSH3 p.Ala60Pro variant was identified in 1 of 126 proband chromosomes (frequency: 0.0079) from CRC specimens collected from Iranian, Shirazi (Iranian Caucasians) (Ashktorab_2017_28002797). The variant was also identified in dbSNP (ID: rs2001675) and MutDB. The variant was not identified in ClinVar, Clinvitae, COGR, Cosmic, LOVD 3.0, UMD-LSDB, Zhejiang University Database, Mismatch Repair Genes Variant Database, ADPKD Mutation Database, PKD1-LOVD, RWTH AAachen University ARPKD database, IARC TP53 Database, or Insight Hereditary Tumors Database. The variant was identified in control databases in 1612 of 135934 chromosomes (27 homozygous) at a frequency of 0.01186 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Ashkenazi Jewish in 122 of 5708 chromosomes (freq: 0.02137), European (non-Finnish) in 1022 of 61450 chromosomes (freq: 0.01663), Other in 46 of 3482 chromosomes (freq: 0.01321), South Asian in 178 of 16450 chromosomes (freq: 0.01082), Latino in 102 of 16548 chromosomes (freq: 0.006164), African in 42 of 8462 chromosomes (freq: 0.004963), European (Finnish) in 73 of 14892 chromosomes (freq: 0.004902) and East Asian in 27 of 8942 chromosomes (freq: 0.003019). Ashktorab et al. identified a variant at loci 79950724 with a G to C change in the MutS_I domain with a frequency of 0.02 (1/63, heterozygous) (Ashktorab_2017_28002797). This variant in MSH3 is predicted by in silico functional analysis to disrupt the MSH2-MSH3 association to form the MutSβ complex which would result in a defective DNA mismatch repair. It appears to suggest altered static interactions within the MSH2-MSH3 heterodimers. The variant occurs at the site of MSH2 binding, and is likely to disturb the complex formed by MSH3 with MSH2. The p.Ala60 residue is not conserved in mammals and computational analyses (SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. References: Ashktorab, Hassan, et al. "Targeted exome sequencing reveals distinct pathogenic variants in Iranians with colorectal cancer." Oncotarget 8.5 (2017): 7852.

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