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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
SLC44A2 ENST00000335757 39.52 29.21 32.56 0.90 1.13 0.87 1.77 1.35 1.63
TUBE1 ENST00000368662 39.52 30.67 33.25 0.90 1.05 0.87 1.77 1.38 1.70
ADRM1 ENST00000253003 39.53 4.09 19.85 0.90 3.24 1.48 1.77 0.32 0.85
ZMAT5 ENST00000397781 39.53 67.94 53.15 0.90 0.52 0.61 1.77 1.17 1.87
SNX13 ENST00000428135 39.54 16.90 26.34 0.90 1.64 1.00 1.77 0.71 1.27
KBTBD3 ENST00000526793 39.54 44.21 40.16 0.90 0.62 0.82 1.77 1.95 1.99
IGSF9B ENST00000533871 39.55 11.94 23.80 0.90 2.09 1.11 1.76 0.59 1.03
GPS1 ENST00000392358 39.55 7.88 21.85 0.90 2.54 1.20 1.76 0.44 0.95
AKAP8L ENST00000397410 39.56 22.01 28.91 0.90 1.48 0.81 1.76 0.81 1.31
DPCD ENST00000370151 39.56 66.81 52.51 0.90 0.54 0.61 1.76 1.23 1.91
DNAH5 ENST00000265104 39.57 35.35 35.60 0.90 0.77 0.86 1.76 1.57 1.77
CTAGE5 ENST00000396158 39.57 29.78 32.87 0.90 1.13 0.85 1.76 1.40 1.67
DPH2 ENST00000255108 39.58 53.44 45.16 0.90 0.65 0.70 1.75 1.70 2.00
PRR11 ENST00000262293 39.58 51.51 43.95 0.90 0.63 0.61 1.75 1.87 2.02
FOXD2 ENST00000334793 39.59 74.86 57.13 0.90 0.53 0.52 1.75 0.95 1.70
CIB3 ENST00000269878 39.60 90.20 66.56 0.90 0.25 0.51 1.75 0.38 1.20
UFC1 ENST00000368003 39.60 49.84 43.09 0.90 0.66 0.65 1.75 2.02 2.01
CC2D2B ENST00000410012 39.61 49.73 43.05 0.90 0.66 0.66 1.75 2.02 2.02
C6orf136 ENST00000293604 39.61 15.21 25.50 0.90 1.90 1.05 1.76 0.67 1.19
VARS2 ENST00000541562 39.62 36.41 36.13 0.90 0.82 0.87 1.76 1.63 1.79
PQLC2 ENST00000375153 39.62 55.38 46.21 0.90 0.58 0.67 1.75 1.61 1.94
METTL24 ENST00000338882 39.63 73.18 56.15 0.90 0.54 0.49 1.75 1.02 1.77
DBR1 ENST00000260803 39.63 55.92 46.43 0.90 0.49 0.67 1.76 1.56 1.92
CSRP2BP ENST00000435364 39.64 45.65 40.81 0.90 0.75 0.80 1.75 2.01 2.04
PLCH2 ENST00000449969 39.64 47.38 41.74 0.90 0.66 0.72 1.75 2.01 2.00

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