ClinVar Miner

Submissions for variant NM_003995.4(NPR2):c.2105T>A (p.Met702Lys)

gnomAD frequency: 0.00010  dbSNP: rs200129431
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002066177 SCV002345076 likely benign Acromesomelic dysplasia 1, Maroteaux type; Tall stature-scoliosis-macrodactyly of the great toes syndrome 2025-01-30 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004702530 SCV005204399 uncertain significance not specified 2024-06-12 criteria provided, single submitter clinical testing Variant summary: NPR2 c.2105T>A (p.Met702Lys) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00026 in 251378 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in NPR2 causing NPR2-Related Disorders, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.2105T>A in individuals affected with NPR2-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 760980). Based on the evidence outlined above, the variant was classified as uncertain significance.
PreventionGenetics, part of Exact Sciences RCV004533603 SCV004720258 likely benign NPR2-related disorder 2019-06-10 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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