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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
RCOR1 ENST00000262241 12.30 1.48 4.19 1.68 3.91 3.77 0.60 0.26 0.23
KIF1A ENST00000498729 3.32 1.47 0.80 3.86 3.91 4.54 0.30 0.26 0.21
TIAL1 ENST00000369093 0.76 1.47 0.21 4.37 3.91 4.86 0.19 0.26 0.18
CTIF ENST00000382998 30.22 1.46 13.46 1.02 3.92 2.05 1.61 0.26 0.57
TPR ENST00000367478 10.33 1.46 3.34 2.04 3.92 3.90 0.54 0.26 0.23
SUFU ENST00000369902 9.94 1.45 3.14 2.07 3.92 3.92 0.50 0.26 0.24
RUVBL2 ENST00000595090 21.95 1.45 9.10 1.52 3.93 2.35 1.03 0.26 0.38
EZH2 ENST00000320356 2.93 1.44 0.69 3.91 3.93 4.60 0.30 0.26 0.20
PAFAH1B1 ENST00000397195 4.19 1.44 1.04 3.70 3.93 4.44 0.30 0.26 0.21
TRPS1 ENST00000395715 11.07 1.43 3.64 1.85 3.94 3.84 0.59 0.26 0.23
CELF2 ENST00000450189 0.61 1.43 0.15 4.35 3.94 4.84 0.19 0.27 0.18
SALL4 ENST00000217086 34.69 1.39 15.87 0.95 3.94 1.77 1.80 0.27 0.66
NAA25 ENST00000261745 3.91 1.42 0.95 3.79 3.94 4.45 0.30 0.27 0.21
ANKRD11 ENST00000301030 27.45 1.38 12.01 1.23 3.95 2.29 1.41 0.27 0.47
MDM4 ENST00000367182 4.09 1.42 1.02 3.73 3.95 4.46 0.31 0.27 0.21
ZCCHC6 ENST00000375963 15.92 1.38 5.92 1.52 3.95 3.29 0.79 0.27 0.29
TBL1XR1 ENST00000430069 1.50 1.41 0.34 4.31 3.95 4.81 0.20 0.27 0.18
SMARCA1 ENST00000371122 22.94 1.37 9.63 1.42 3.95 2.26 1.07 0.27 0.40
ARID5B ENST00000279873 6.30 1.40 1.75 3.02 3.95 4.22 0.36 0.27 0.23
REV3L ENST00000358835 18.25 1.37 7.17 1.51 3.96 2.86 0.90 0.27 0.34
UTP15 ENST00000296792 16.34 1.40 6.14 1.48 3.96 3.21 0.81 0.27 0.30
BCOR ENST00000378444 23.60 1.33 10.03 1.35 3.96 2.26 1.10 0.27 0.42
SETBP1 ENST00000282030 11.87 1.36 3.95 1.63 3.96 3.76 0.60 0.27 0.23
MTA1 ENST00000331320 5.98 1.39 1.63 3.06 3.96 4.28 0.34 0.27 0.23
DHX15 ENST00000336812 0.05 1.30 0.06 4.59 3.96 4.86 0.15 0.27 0.15

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