splice region variant & 5 prime utr variant  (5 PRIME)

Journal: Animals : an Open Access Journal from MDPI

Article Title: Unveiling Genetic Potential for Equine Meat Production: A Bioinformatics Approach

doi: 10.3390/ani14162441

Figure Lengend Snippet: Summary of prioritized SNP markers, their associated genes, variant consequences, and the criteria for their prioritization. A ✓ indicates the presence of the respective characteristic: potential effect on protein function, GERP > 2 (indicating evolutionary conservation), location within a constrained element, or location within an orthologous regulatory element. SNPs that differ between Percheron and American Miniature horse breeds are marked in bold.

Article Snippet: Variants that may alter protein sequence and function include two missense variants rs68555658 and rs1147724321 (markers UKUL834 and UKUL835) in PCDH7 with GERP scores 2.83 and 3.84, respectively, a stop-lost variant rs1141209077 (marker CUHSNP00004551) in PI4K2B , and a splice donor region variant rs68593800 (marker CUHSNP00004551) in SLIT2 , located in constrained element.

Techniques: Variant Assay, Marker

Journal: Human Genomics

Article Title: Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project

doi: 10.1186/s40246-024-00604-w

Figure Lengend Snippet: Confirmatory RNA sequencing in P1 and P3. For both A and B , in the top panel, paired end reads from the RNA sequencing BAM file are displayed for the proband. In the lower panels, the RNA sequencing read pileup tract is displayed with the novel (orange) and known (blue) junctions annotated in the proband and in aggregated data from GTEx controls, respectively. Beneath, the gene transcript isoforms are displayed. A , RNA sequencing analysis performed on blood in P1 compared to normalized GTEx blood samples (n = 755) (21). The results for ASNS (displaying exon 9 and 10) demonstrate evidence of splice disruption due to a deep intronic indel (indicated by the red box in the proband) with cryptic exon creation and intron 9 read-through. B , RNA sequencing analysis performed on an EBV-transformed lymphoblastoid cell line (LCL) in P3 compared to normalized GTEx lymphocyte samples (n = 174). The results for TCF4 (displaying exon 10 to 13) demonstrate evidence of splice disruption due to a near-splice variant (indicated by the red line in the proband) with skipping of exon 11 in approximately 20% of reads. E, exon

Article Snippet: The first, by the detection of a de novo splice region variant in TCF4 (c.1228 + 3G > T, ENST00000398339), prioritized by eight models in total, submitted by Team 9 (Invitae Moon, model 1 at rank 1), Team 5 (Exomiser, model 1–2 at rank 1 and model 3 at rank 2), and Team 11 (enGenome, model 2 and 4 at rank 1, and model 1 and 3 at rank 2).

Techniques: RNA Sequencing, Disruption, Transformation Assay, Variant Assay