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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
RRAGD ENST00000369415 10.34 14.28 9.83 2.04 2.06 2.30 0.54 0.61 0.40
AKT1 ENST00000554581 10.34 13.20 9.21 2.04 2.06 2.32 0.54 0.60 0.38
PTPN6 ENST00000456013 10.35 2.52 3.78 2.05 3.55 3.79 0.54 0.29 0.24
HELZ ENST00000358691 10.35 0.08 2.71 2.05 4.13 4.01 0.54 0.27 0.23
STAT4 ENST00000392320 10.36 15.31 10.38 2.05 1.90 2.19 0.54 0.67 0.43
TOP2A ENST00000423485 10.36 11.17 8.11 2.05 2.09 2.58 0.54 0.54 0.37
KDM4A ENST00000372396 10.37 3.31 4.13 2.05 3.43 3.79 0.54 0.27 0.24
PHB2 ENST00000535923 10.37 34.96 20.83 2.04 0.76 1.46 0.54 1.55 0.88
TOPORS ENST00000360538 10.38 8.21 6.67 2.04 2.57 3.01 0.54 0.45 0.32
TAB2 ENST00000367456 10.38 1.11 3.18 2.04 4.02 3.90 0.54 0.28 0.24
CDK5R1 ENST00000313401 10.39 17.30 11.52 2.05 1.61 2.19 0.54 0.75 0.45
ASAP2 ENST00000281419 10.39 7.61 6.28 2.05 2.49 3.14 0.54 0.42 0.32
MLLT6 ENST00000325718 10.40 5.07 5.00 2.05 3.21 3.68 0.54 0.33 0.25
USP32 ENST00000300896 10.40 4.33 4.71 2.05 3.27 3.68 0.54 0.32 0.25
FIP1L1 ENST00000337488 10.41 13.96 9.66 2.05 2.05 2.26 0.54 0.60 0.40
PRKCD ENST00000394729 10.41 4.25 4.67 2.05 3.26 3.69 0.54 0.32 0.25
NOG ENST00000332822 10.42 19.88 12.69 2.05 1.43 2.18 0.53 0.73 0.52
SFSWAP ENST00000541286 10.42 3.77 4.38 2.05 3.32 3.72 0.53 0.31 0.24
NABP2 ENST00000380198 10.43 10.56 7.86 2.05 2.16 2.63 0.53 0.52 0.35
ATAD1 ENST00000308448 10.43 41.45 23.99 2.05 0.62 1.09 0.53 1.81 1.05
RAB35 ENST00000229340 10.44 9.21 7.22 2.04 2.47 2.81 0.53 0.47 0.34
PELI1 ENST00000358912 10.44 25.14 15.63 2.04 1.32 1.75 0.53 1.03 0.67
SMG7 ENST00000507469 10.45 6.56 5.78 2.02 2.63 3.31 0.53 0.37 0.28
MDGA2 ENST00000426342 10.45 8.85 7.01 2.02 2.47 2.88 0.53 0.48 0.33
SOCS7 ENST00000577233 10.46 8.13 6.70 2.02 2.53 3.01 0.53 0.44 0.32

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