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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
RARS ENST00000231572 46.49 42.97 43.11 0.56 0.62 0.65 1.80 1.90 2.01
SHKBP1 ENST00000291842 46.50 37.41 40.22 0.56 0.75 0.82 1.80 1.66 2.00
RBM28 ENST00000223073 46.50 42.35 42.73 0.56 0.61 0.70 1.80 1.90 2.02
C1QC ENST00000374639 46.51 50.50 47.24 0.56 0.65 0.67 1.81 1.94 1.87
OSBP2 ENST00000332585 46.51 25.12 33.99 0.56 1.32 0.90 1.81 1.03 1.73
ADCY4 ENST00000310677 46.52 46.38 45.10 0.56 0.73 0.70 1.81 2.04 2.02
LIMCH1 ENST00000313860 46.52 13.44 28.16 0.56 2.05 0.82 1.81 0.60 1.27
PROC ENST00000234071 46.53 43.28 43.27 0.56 0.61 0.65 1.81 1.93 2.00
NIPAL2 ENST00000341166 46.53 76.23 62.19 0.56 0.43 0.48 1.81 0.85 1.45
SPTA1 ENST00000368147 46.54 24.47 33.67 0.56 1.32 0.90 1.81 1.01 1.72
STK11 ENST00000326873 46.54 8.88 25.86 0.56 2.44 1.01 1.82 0.48 1.23
ZNF358 ENST00000597229 46.55 25.74 34.41 0.56 1.24 0.90 1.81 1.05 1.76
P2RX1 ENST00000225538 46.55 65.78 55.83 0.56 0.54 0.51 1.81 1.22 1.75
GALC ENST00000261304 46.56 52.51 48.41 0.56 0.66 0.67 1.81 1.83 1.87
TECPR2 ENST00000359520 46.56 14.30 28.58 0.56 2.05 0.80 1.81 0.61 1.35
ARHGAP10 ENST00000336498 46.57 51.08 47.61 0.56 0.66 0.65 1.81 1.92 1.87
DAK ENST00000394900 46.57 59.27 52.15 0.56 0.49 0.61 1.81 1.42 1.90
CTD-3074O7.11 ENST00000419755 46.58 48.75 46.32 0.56 0.63 0.67 1.82 2.00 1.90
GOLGA4 ENST00000356847 46.58 24.97 33.96 0.56 1.33 0.90 1.82 1.05 1.73
CTNNA3 ENST00000433211 46.59 45.28 44.46 0.56 0.70 0.61 1.82 1.97 2.04
LYPD6 ENST00000334166 46.59 78.05 63.51 0.56 0.43 0.49 1.82 0.76 1.39
OPRL1 ENST00000349451 46.60 30.97 37.04 0.56 1.04 0.80 1.82 1.36 1.95
AKAP1 ENST00000337714 46.60 17.47 30.22 0.56 1.58 0.81 1.81 0.74 1.44
FYCO1 ENST00000296137 46.61 47.58 45.80 0.56 0.61 0.68 1.81 2.00 1.98
GEMIN5 ENST00000285873 46.61 39.01 41.03 0.56 0.70 0.76 1.81 1.64 2.04

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