PVS1
This is a missense variant, not a null variant, and SpliceAI predicts no splice impact with a maximum delta score of 0.00.
PS1
No previously established pathogenic LZTR1 variant with the same amino acid change was identified in the available records, so PS1 cannot be applied from the current evidence.
PS2
No confirmed de novo occurrence with maternity and paternity confirmation was identified for this variant, so PS2 cannot be applied from the current evidence.
PS3
No approved variant-specific functional study was identified for this variant, so PS3 cannot be applied from the current evidence.
PS4
No published enrichment study, case series, or scored proband dataset was identified for this variant.
PM3
No evidence was identified that this variant was observed in trans with a pathogenic variant in a recessive case, so PM3 cannot be applied from the current evidence.
PM4
This is a missense substitution and does not cause a protein length change from an in-frame insertion, in-frame deletion, or stop-loss variant, so PM4 is not met.
PM5
No pathogenic or likely pathogenic missense change at codon 806 was identified in the available records, so PM5 cannot be applied from the current evidence.
PM6
No assumed de novo observation without full parental confirmation was identified for this variant, so PM6 cannot be applied from the current evidence.
PP1
No segregation data were identified for this variant, so PP1 cannot be applied from the current evidence.
PP3
REVEL is 0.174, which is below the LZTR1 PP3 threshold of 0.7, SpliceAI predicts no significant splice impact with a maximum delta score of 0.00, and BayesDel is -0.202983.
