Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005460.4(SNCAIP):c.1862G>A(p.Arg621His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R621C) has been classified as Likely benign.
SNCAIP (HGNC:11139): (synuclein alpha interacting protein) This gene encodes a protein containing several protein-protein interaction domains, including ankyrin-like repeats, a coiled-coil domain, and an ATP/GTP-binding motif. The encoded protein interacts with alpha-synuclein in neuronal tissue and may play a role in the formation of cytoplasmic inclusions and neurodegeneration. A mutation in this gene has been associated with Parkinson's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
Review Status: criteria provided, single submitter
Collection Method: clinical testing
The c.1862G>A (p.R621H) alteration is located in exon 10 (coding exon 9) of the SNCAIP gene. This alteration results from a G to A substitution at nucleotide position 1862, causing the arginine (R) at amino acid position 621 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -