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Table 3 Results of identification of causative variants for the CAGI6 SickKids challenge

From: Explicable prioritization of genetic variants by integration of rule-based and machine learning algorithms for diagnosis of rare Mendelian disorders

Causal gene

Causal variants found by 3ASC

PVS1 rule applied by 3ASC

Decreased gene expression

HDAC8

Found

Applied

Found*

CASK

Found

Applied

Found**

HMGA2

Found

Applied

Not found

PDHA1

Found

Applied

Not found

NKX6-2

Found

Applied

Not found

FOXG1

Found

Applied

Not found

KCNB1

Found

Not applied

Not found

COL12A1

Found

Not applied

Not found

EPG5

Found

Not applied

Not found

H3F3B

Found

Not applied

Not found

ZNF711

Not found

Not applied

Not found

DSG2

Not found

Not applied

Not found

SMAD6

Not found

Not applied

Not found

FBXW7

Not found

Not applied

Not found

  1. The evidence of gene causality is indicated in bold
  2. *log2 transformation for RNAseq read count of the affected sample was compared with the distribution of those of 244 other samples (Z-score = − 10.15)
  3. **log2 transformation for RNAseq read count of the affected sample showed Z-score of − 2.04
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Human Genomics

ISSN: 1479-7364