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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
EFNB1 ENST00000204961 18.08 18.88 16.29 1.53 1.53 1.71 0.90 0.76 0.66
PITX3 ENST00000370002 18.09 23.42 18.77 1.53 1.42 1.57 0.90 0.93 0.82
AR ENST00000374690 18.09 12.64 12.90 1.53 2.10 2.10 0.90 0.58 0.53
TTC39A ENST00000413473 18.10 24.45 19.26 1.53 1.32 1.54 0.90 1.00 0.85
CKS2 ENST00000314355 18.10 48.89 31.69 1.53 0.63 0.89 0.90 2.04 1.58
NRXN1 ENST00000404971 18.11 7.14 10.17 1.53 2.58 2.24 0.90 0.37 0.42
PFDN1 ENST00000261813 18.11 24.89 19.50 1.53 1.32 1.54 0.91 1.06 0.83
RPS4X ENST00000316084 18.12 15.63 14.61 1.53 1.87 1.97 0.91 0.68 0.59
DIP2B ENST00000301180 18.12 10.40 11.86 1.53 2.24 2.24 0.91 0.50 0.46
SFRP2 ENST00000274063 18.13 56.33 35.43 1.52 0.52 0.87 0.91 1.55 1.76
AHSA1 ENST00000216479 18.13 3.16 8.01 1.52 3.46 2.59 0.91 0.28 0.37
MACROD2 ENST00000217246 18.14 21.47 17.71 1.52 1.42 1.66 0.91 0.80 0.78
XRN1 ENST00000264951 18.14 4.88 8.85 1.52 3.27 2.47 0.91 0.31 0.38
SKOR1 ENST00000341418 18.15 38.84 26.65 1.52 0.68 0.99 0.91 1.66 1.25
USF1 ENST00000368021 18.16 30.87 22.70 1.52 1.08 1.18 0.91 1.36 0.97
MTM1 ENST00000370396 18.16 4.98 8.93 1.52 3.25 2.48 0.91 0.32 0.38
BEND7 ENST00000341083 18.17 33.69 23.94 1.52 0.84 1.09 0.91 1.56 1.04
RUFY1 ENST00000319449 18.17 33.89 24.06 1.52 0.84 1.10 0.91 1.55 1.06
KIF21A ENST00000361418 18.18 20.39 17.14 1.52 1.43 1.64 0.90 0.76 0.73
SORT1 ENST00000256637 18.18 6.41 9.80 1.52 2.64 2.29 0.90 0.37 0.40
HIST1H2BK ENST00000396891 18.19 97.24 57.69 1.52 0.24 0.49 0.90 0.19 1.68
ELL2 ENST00000237853 18.19 9.61 11.57 1.51 2.48 2.21 0.90 0.50 0.45
ZNF436 ENST00000314011 18.20 46.00 30.29 1.51 0.77 0.84 0.90 2.02 1.44
LAMTOR2 ENST00000368305 18.20 48.15 31.41 1.51 0.63 0.87 0.90 1.97 1.55
NTM ENST00000425719 18.21 35.18 24.76 1.51 0.76 1.04 0.90 1.58 1.10

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