See Table A. Genes and Databases for chromosome locus and protein.

See Molecular Genetics for information on variants detected in this gene.

Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. Variants may include small intragenic deletions/insertions and missense, nonsense, and splice site variants; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.

Of individuals evaluated for NF1 without an identifiable NF1 pathogenic variant, 3%-25% had an identifiable SPRED1 pathogenic variant [Brems et al 2007, Messiaen et al 2009, Pasmant et al 2009, Spurlock et al 2009]. Sequence analysis should identify the majority of individuals without whole-gene deletions, although it is estimated that approximately 1%-2% could have deep intronic variants which could be missed; however, this has not been reported.

Testing that identifies exon or whole-gene deletions/duplications not detectable by sequence analysis of the coding and flanking intronic regions of genomic DNA. Methods used may include a range of techniques such as quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and chromosomal microarray (CMA) that includes this gene/chromosome segment.

Spencer et al [2011] report that deletions comprise approximately 10% of SPRED1 pathogenic variants and include multiexon deletions and whole SPRED1 gene deletions

Sequence analysis in combination with deletion/duplication analysis should identify the majority of individuals, although it is estimated that approximately 1% could have deep intronic variants that could be missed; however, this has not been reported.