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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
ZNF483 ENST00000309235 16.53 14.16 12.88 1.43 2.07 2.11 0.81 0.60 0.53
GANAB ENST00000346178 16.54 11.02 11.45 1.43 2.10 2.21 0.81 0.52 0.45
R3HDM2 ENST00000347140 16.54 4.42 7.84 1.43 3.27 2.63 0.81 0.32 0.35
ZMYND19 ENST00000298585 16.55 15.79 13.85 1.43 1.90 2.10 0.81 0.69 0.59
GULP1 ENST00000409580 16.55 22.11 17.17 1.43 1.52 1.64 0.81 0.83 0.73
PRELID1 ENST00000303204 16.56 37.44 25.07 1.43 0.76 1.05 0.81 1.66 1.15
UBE2O ENST00000319380 16.56 2.98 7.12 1.43 3.47 2.87 0.81 0.28 0.33
RBFOX2 ENST00000438146 16.57 5.59 8.44 1.43 2.99 2.53 0.81 0.33 0.38
NEO1 ENST00000339362 16.57 15.72 13.80 1.43 1.87 2.07 0.81 0.69 0.57
KCTD4 ENST00000405872 16.58 64.93 39.09 1.43 0.48 0.77 0.81 1.24 2.06
AMPD2 ENST00000256578 16.58 32.14 22.55 1.43 0.87 1.15 0.81 1.46 0.97
NETO1 ENST00000327305 16.59 26.67 19.63 1.43 1.18 1.53 0.82 1.12 0.85
TMEM135 ENST00000305494 16.60 17.65 14.88 1.43 1.58 1.94 0.82 0.73 0.63
RND3 ENST00000375734 16.60 12.86 12.31 1.44 2.07 2.25 0.82 0.59 0.50
ZDHHC16 ENST00000393760 16.61 37.65 25.23 1.44 0.78 1.05 0.82 1.70 1.15
SRGAP1 ENST00000355086 16.61 10.12 11.00 1.44 2.33 2.20 0.82 0.49 0.44
DUSP14 ENST00000487847 16.62 62.48 37.77 1.44 0.53 0.84 0.82 1.31 2.01
OTUD7B ENST00000369135 16.62 23.24 17.83 1.44 1.43 1.67 0.82 0.92 0.77
FOXP3 ENST00000376207 16.63 5.89 8.58 1.46 2.82 2.53 0.82 0.35 0.36
NUS1 ENST00000368494 16.63 8.55 10.13 1.46 2.52 2.24 0.82 0.47 0.41
OSGIN2 ENST00000451899 16.64 21.00 16.66 1.46 1.44 1.70 0.83 0.83 0.70
ETNK1 ENST00000266517 16.64 16.10 14.08 1.46 1.82 2.04 0.83 0.69 0.60
SLC25A3 ENST00000228318 16.65 31.12 22.00 1.46 1.01 1.19 0.83 1.36 0.97
MED25 ENST00000312865 16.65 32.34 22.65 1.46 0.86 1.18 0.83 1.46 0.96
EBF2 ENST00000520164 16.66 5.57 8.46 1.46 2.99 2.52 0.83 0.33 0.37

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