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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
ITPR2 ENST00000381340 19.89 30.80 23.44 1.53 1.06 1.19 0.99 1.37 1.01
COPB1 ENST00000249923 19.90 6.45 10.77 1.53 2.63 2.19 0.99 0.37 0.43
GPR4 ENST00000323040 19.90 44.43 30.35 1.53 0.62 0.81 0.99 1.97 1.45
AURKA ENST00000395909 19.91 18.24 16.92 1.53 1.49 1.67 1.00 0.74 0.71
RAB7L1 ENST00000367139 19.91 39.97 28.15 1.53 0.63 0.81 1.00 1.68 1.27
TTC17 ENST00000039989 19.92 7.43 11.38 1.53 2.54 2.20 1.00 0.39 0.45
RNF19B ENST00000373456 19.92 15.46 15.50 1.53 1.87 1.81 1.00 0.67 0.67
NUP210L ENST00000368559 19.93 17.58 16.60 1.52 1.58 1.72 1.00 0.73 0.70
PTCHD1 ENST00000379361 19.93 10.82 12.91 1.52 2.13 2.10 1.00 0.50 0.53
KIAA1244 ENST00000251691 19.94 6.37 10.75 1.52 2.67 2.19 1.00 0.37 0.43
GALNTL6 ENST00000506823 19.94 45.01 30.73 1.52 0.68 0.78 1.01 1.97 1.48
TMEM150A ENST00000409668 19.95 40.44 28.38 1.52 0.62 0.78 1.01 1.77 1.29
ENO2 ENST00000535366 19.95 24.96 20.58 1.52 1.32 1.48 1.00 1.07 0.88
FAM160A2 ENST00000265978 19.96 12.46 13.89 1.52 2.06 2.10 1.00 0.59 0.59
NCOA7 ENST00000368357 19.96 25.84 21.05 1.52 1.21 1.43 1.00 1.07 0.90
BRAP ENST00000419234 19.97 30.95 23.56 1.52 1.05 1.19 1.00 1.35 1.01
TMEM248 ENST00000341567 19.97 24.97 20.60 1.52 1.32 1.48 0.99 1.05 0.88
CNOT10 ENST00000454516 19.98 12.78 14.12 1.52 2.09 2.02 1.00 0.59 0.59
FAM84B ENST00000304916 19.98 71.52 44.23 1.52 0.53 0.62 1.00 1.07 2.04
NAE1 ENST00000290810 19.99 49.91 33.10 1.52 0.66 0.87 1.00 2.02 1.68
SREBF1 ENST00000355815 19.99 21.55 18.79 1.52 1.43 1.57 1.00 0.81 0.82
RAB22A ENST00000244040 20.00 39.06 27.68 1.52 0.70 0.94 1.00 1.63 1.27
PIK3R4 ENST00000356763 20.00 17.67 16.69 1.52 1.57 1.70 1.00 0.73 0.70
ALAS2 ENST00000330807 20.01 4.78 9.95 1.53 3.28 2.29 1.00 0.32 0.42
TRADD ENST00000345057 20.01 34.76 25.46 1.53 0.77 1.02 1.00 1.55 1.18

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