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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
TMEM132B ENST00000299308 34.22 9.11 19.68 0.95 2.47 1.53 1.78 0.47 0.85
PVRL1 ENST00000264025 34.23 29.17 29.88 0.95 1.13 0.86 1.78 1.34 1.44
POLDIP3 ENST00000252115 34.23 22.56 26.50 0.95 1.48 0.99 1.78 0.85 1.25
SC5D ENST00000264027 34.24 52.41 41.56 0.95 0.63 0.73 1.78 1.83 2.01
AFAP1L2 ENST00000304129 34.24 21.96 26.27 0.95 1.47 1.01 1.78 0.81 1.26
N4BP2L1 ENST00000380130 34.25 21.63 26.10 0.95 1.44 0.99 1.78 0.81 1.25
VASH2 ENST00000366965 34.25 34.60 32.64 0.95 0.80 0.87 1.78 1.54 1.63
SPEG ENST00000312358 34.26 12.20 21.36 0.96 2.07 1.35 1.78 0.58 0.91
FOXA3 ENST00000302177 34.26 29.02 29.83 0.96 1.15 0.87 1.78 1.31 1.43
ABCC4 ENST00000376887 34.27 24.90 27.74 0.96 1.32 0.91 1.78 1.07 1.27
FAM81A ENST00000288228 34.28 23.97 27.26 0.96 1.37 0.99 1.78 0.95 1.25
FRMD7 ENST00000298542 34.28 18.97 24.72 0.96 1.52 1.05 1.78 0.76 1.10
PTTG1 ENST00000393964 34.29 75.07 54.19 0.96 0.51 0.59 1.78 0.91 1.73
BHLHE41 ENST00000242728 34.29 6.42 18.32 0.96 2.63 1.66 1.78 0.37 0.80
ENPP4 ENST00000321037 34.30 38.02 34.42 0.96 0.77 0.90 1.78 1.70 1.76
NPY ENST00000407573 34.30 57.88 44.65 0.96 0.57 0.62 1.78 1.48 2.06
SPRY4 ENST00000344120 34.31 67.42 49.83 0.97 0.56 0.65 1.78 1.20 1.89
TARS ENST00000455217 34.31 39.92 35.34 0.97 0.63 0.87 1.78 1.69 1.76
GRAMD3 ENST00000513040 34.32 64.62 48.32 0.97 0.48 0.67 1.78 1.22 1.89
SLC52A3 ENST00000217254 34.32 43.22 36.99 0.97 0.62 0.78 1.78 1.91 1.94
SPATA9 ENST00000274432 34.33 73.66 53.41 0.97 0.52 0.62 1.78 1.03 1.84
JUP ENST00000393931 34.33 31.16 30.96 0.97 1.01 0.81 1.78 1.36 1.51
NR1H3 ENST00000467728 34.34 17.07 23.78 0.97 1.62 1.13 1.79 0.74 1.03
ZNF496 ENST00000294753 34.34 8.99 19.68 0.97 2.44 1.53 1.79 0.47 0.85
RAVER1 ENST00000293677 34.35 17.78 24.08 0.97 1.53 1.10 1.79 0.73 1.06

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