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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
LIN37 ENST00000301159 22.47 45.52 32.20 1.46 0.72 0.91 1.04 1.99 1.60
DYNLRB1 ENST00000357156 22.48 62.94 40.91 1.46 0.51 0.78 1.04 1.31 2.05
ELOVL4 ENST00000369816 22.48 19.05 18.78 1.46 1.52 1.57 1.05 0.76 0.82
PI4KA ENST00000255882 22.49 21.96 20.29 1.46 1.47 1.47 1.05 0.81 0.89
CLIC1 ENST00000375780 22.49 71.07 45.49 1.46 0.49 0.70 1.05 1.07 1.97
DCLRE1B ENST00000369563 22.50 23.61 21.17 1.44 1.39 1.40 1.05 0.93 0.90
CPOX ENST00000264193 22.50 27.69 23.19 1.44 1.27 1.19 1.05 1.19 1.02
KCNJ12 ENST00000583088 22.51 55.95 37.46 1.46 0.49 0.86 1.05 1.56 2.01
NUDC ENST00000321265 22.51 17.00 17.67 1.46 1.63 1.67 1.05 0.73 0.78
CRMP1 ENST00000324989 22.52 10.87 14.43 1.46 2.11 2.00 1.05 0.50 0.59
KIF2C ENST00000372224 22.52 28.19 23.49 1.46 1.18 1.18 1.05 1.20 1.01
SWT1 ENST00000367500 22.53 8.33 13.00 1.46 2.52 2.09 1.05 0.45 0.52
CCNB1 ENST00000256442 22.53 27.80 23.25 1.46 1.23 1.19 1.05 1.18 1.01
MGAT2 ENST00000305386 22.54 39.11 28.99 1.46 0.70 0.81 1.05 1.63 1.31
POLE3 ENST00000374171 22.55 69.37 44.49 1.46 0.56 0.61 1.05 1.14 2.04
TMEM17 ENST00000335390 22.55 70.99 45.49 1.46 0.49 0.70 1.05 1.07 1.97
HPN ENST00000262626 22.56 5.77 11.78 1.46 2.87 2.21 1.05 0.34 0.46
UBXN4 ENST00000272638 22.56 23.75 21.24 1.46 1.38 1.40 1.05 0.93 0.89
GORASP2 ENST00000234160 22.57 18.37 18.40 1.46 1.48 1.64 1.05 0.75 0.80
DLL1 ENST00000366756 22.57 0.98 9.23 1.46 4.08 2.32 1.05 0.28 0.38
MGAT4A ENST00000264968 22.58 33.24 26.07 1.46 0.82 0.99 1.05 1.49 1.25
ALS2 ENST00000264276 22.58 24.26 21.55 1.46 1.30 1.28 1.05 0.99 0.93
RXRG ENST00000359842 22.59 24.49 21.69 1.46 1.32 1.25 1.05 1.01 0.92
RWDD2A ENST00000369724 22.59 82.89 51.91 1.46 0.32 0.62 1.05 0.49 1.94
FAM175B ENST00000298492 22.60 32.34 25.56 1.46 0.86 1.05 1.05 1.46 1.19

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