The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000251.3(MSH2):c.929T>G (p.Leu310Arg)

CA022554

91246 (ClinVar)

Gene: MSH2
Condition: Lynch syndrome 1
Inheritance Mode: Autosomal dominant inheritance
UUID: e574d7b2-f9f7-4437-89e2-b0b6f4487582
Approved on: 2024-10-11
Published on: 2024-10-11

HGVS expressions

NM_000251.3:c.929T>G
NM_000251.3(MSH2):c.929T>G (p.Leu310Arg)
NC_000002.12:g.47414405T>G
CM000664.2:g.47414405T>G
NC_000002.11:g.47641544T>G
CM000664.1:g.47641544T>G
NC_000002.10:g.47495048T>G
NG_007110.2:g.16282T>G
ENST00000644900.2:c.929T>G
ENST00000233146.7:c.929T>G
ENST00000543555.6:c.731T>G
ENST00000644092.1:c.929T>G
ENST00000645339.1:c.929T>G
ENST00000645506.1:c.929T>G
ENST00000646415.1:c.929T>G
ENST00000233146.6:c.929T>G
ENST00000406134.5:c.929T>G
ENST00000543555.5:c.731T>G
ENST00000610696.4:c.929T>G
ENST00000613514.4:c.929T>G
ENST00000617333.3:c.929T>G
ENST00000617938.4:c.929T>G
ENST00000621359.2:c.929T>G
NM_000251.2:c.929T>G
NM_001258281.1:c.731T>G

Pathogenic

Met criteria codes 5
PP4_Moderate PM5 PM2_Supporting PP1_Strong PP3_Moderate

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP
The NM_000251.3(MSH2):c.929T>G (p.Leu310Arg) variant is a missense variant replacing Leucin 310 to Arginin. The variant has been reported to co-segregate with disease in pedigree(s) with a combined* Bayes Likelihood Ratio >18.72 in ≥2 families (PMID: 30376427, 33848333) (PP1_STR). The variant is a missense variant with MAPP+PolyPhen-2 prior probability for pathogenicity >0.81 as per http://priors.hci.utah.edu/PRIORS (PP3_MOD). The variant is a missense change at an amino acid residue where a different missense change was classified by this VCEP as Pathogenic on the protein level; p.Leu310Pro classified as Class 5 by InSiGHT (PM5). The variant has been detected in at least 2 independent CRC/Endometrial MSI-H tumours using a standard panel of 5-10 markersg and/or loss of MMR protein expression consistent with the variant location (PP4_MOD). The variant is not reported in gnomAD v4.1 (PM2_SUP). In summary, this variant meets the criteria to be classified as pathogenic for autosomal-dominant inherited Lynch-syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis: criteria PM5, PP1_strong, PP4_moderate, PP3_moderate and PM2_supporting applied. (VCEP specifications version 1)
Met criteria codes
PP4_Moderate
At least 2 independent CRC/Endometrial MSI-H tumours using a standard panel of 5-10 markersg and/or loss of MMR protein expression consistent with the variant location
PM5
Missense change at an amino acid residue where a different missense change was classified by this VCEP as Pathogenic on the protein level; p.Leu310Pro classified as Class 5 by InSiGHT: (PM5 met)
PM2_Supporting
This variant is absent from gnomAD v2.1.1 and gnomAD v4.1 (PM2_Supporting)
PP1_Strong
The variant has been reported to co-segregate with disease in pedigree(s) with a combined* Bayes Likelihood Ratio >18.72 in ≥2 families (PMID: 30376427, 33848333); PP1_strong met
PP3_Moderate
prior probability of 0.95 exceeds the threshold of 0.81 (PP3_MOD met) hci-priors.hci.utah.edu/PRIORS/
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