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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
ZNF595 ENST00000526473 100.00 67.01 86.68 0.10 0.53 0.30 0.14 1.24 0.33
NBPF1 ENST00000430580 99.99 57.03 81.87 0.10 0.56 0.37 0.14 1.52 0.46
TCEB3C ENST00000330682 99.99 99.68 99.93 0.10 0.17 0.12 0.14 0.11 0.04
RP11-347C12.3 ENST00000550538 99.98 72.69 89.46 0.10 0.47 0.18 0.14 1.04 0.24
MUC2 ENST00000441003 99.98 18.52 59.57 0.10 1.49 0.49 0.14 0.76 1.69
C10orf67 ENST00000323327 99.97 87.29 96.36 0.10 0.22 0.07 0.14 0.41 0.09
CTD-2140B24.4 ENST00000540096 99.97 49.83 78.13 0.10 0.66 0.39 0.14 2.02 0.55
SCML1 ENST00000380041 99.96 11.73 55.51 0.10 2.07 0.51 0.14 0.57 1.74
MUC12 ENST00000536621 99.96 81.41 93.43 0.10 0.33 0.11 0.14 0.54 0.15
C5orf60 ENST00000448248 99.95 85.06 95.24 0.10 0.25 0.08 0.14 0.45 0.10
IL13 ENST00000304506 99.95 85.21 95.29 0.10 0.25 0.08 0.14 0.45 0.10
CD58 ENST00000369489 99.94 34.44 69.32 0.10 0.80 0.43 0.14 1.56 0.98
KLRD1 ENST00000336164 99.94 65.89 86.15 0.10 0.54 0.33 0.14 1.23 0.33
RFPL4A ENST00000434937 99.93 87.56 96.55 0.10 0.23 0.07 0.14 0.37 0.07
TCEB3CL ENST00000451265 99.93 99.20 99.98 0.10 0.15 0.13 0.14 0.13 0.04
SCGB2A1 ENST00000244930 99.92 75.19 90.63 0.10 0.49 0.15 0.14 0.91 0.20
C11orf72 ENST00000333139 99.92 99.44 99.89 0.10 0.16 0.12 0.14 0.12 0.04
CD4 ENST00000011653 99.91 39.67 72.48 0.10 0.68 0.44 0.14 1.66 0.83
C1orf61 ENST00000368243 99.91 91.26 98.04 0.10 0.23 0.09 0.14 0.34 0.05
ZNF93 ENST00000343769 99.90 89.98 97.55 0.10 0.25 0.08 0.14 0.37 0.07
MUC13 ENST00000311075 99.90 37.26 70.95 0.10 0.76 0.43 0.14 1.66 0.85
MUC21 ENST00000376296 99.89 78.06 91.78 0.12 0.43 0.14 0.14 0.76 0.18
MSMB ENST00000358559 99.89 82.97 94.18 0.12 0.32 0.09 0.14 0.49 0.12
CD59 ENST00000395850 99.88 53.36 79.95 0.12 0.66 0.35 0.14 1.70 0.52
CD46 ENST00000322875 99.88 48.85 77.58 0.12 0.63 0.37 0.14 2.03 0.56

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