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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
LUZP1 ENST00000302291 30.74 20.45 23.72 0.96 1.43 1.15 1.63 0.76 1.02
EDAR ENST00000258443 30.74 50.95 39.22 0.96 0.65 0.78 1.63 1.93 2.05
ERGIC2 ENST00000360150 30.75 33.26 30.16 0.96 0.84 0.81 1.63 1.50 1.45
TMEM9 ENST00000367330 30.75 69.00 48.75 0.96 0.54 0.68 1.64 1.15 1.85
SLC7A14 ENST00000231706 30.76 28.75 27.91 0.96 1.15 0.85 1.64 1.29 1.29
PTAFR ENST00000373857 30.76 50.67 39.06 0.96 0.63 0.78 1.64 1.95 2.06
ONECUT1 ENST00000305901 30.77 30.99 29.04 0.96 1.04 0.82 1.64 1.36 1.32
SLC13A3 ENST00000279027 30.77 48.71 38.00 0.96 0.63 0.85 1.64 1.99 2.03
SAR1B ENST00000402673 30.78 55.16 41.18 0.96 0.57 0.76 1.63 1.61 2.02
SLC35E3 ENST00000398004 30.78 73.40 51.17 0.96 0.54 0.63 1.63 1.03 1.91
ANKRD44 ENST00000409919 30.79 26.30 26.70 0.96 1.19 1.00 1.63 1.08 1.27
ANO6 ENST00000423947 30.79 62.58 45.40 0.96 0.52 0.70 1.63 1.31 2.01
DHFR ENST00000439211 30.80 47.04 37.19 0.96 0.68 0.81 1.63 1.99 1.97
UGGT1 ENST00000259253 30.80 24.58 25.83 0.96 1.30 1.01 1.63 1.05 1.23
CDR2 ENST00000268383 30.81 55.06 41.12 0.96 0.58 0.76 1.63 1.63 2.04
ZFYVE20 ENST00000253699 30.81 23.20 25.08 0.97 1.43 1.05 1.63 0.91 1.17
MEF2A ENST00000354410 30.82 11.28 19.04 0.97 2.13 1.54 1.63 0.55 0.85
LEAP2 ENST00000296877 30.82 92.60 62.62 0.99 0.29 0.48 1.63 0.31 1.40
CITED1 ENST00000453707 30.83 66.78 47.60 0.99 0.56 0.65 1.63 1.22 1.87
GARS ENST00000389266 30.84 20.21 23.61 0.99 1.43 1.19 1.64 0.74 1.01
WDR77 ENST00000235090 30.84 44.95 36.00 0.99 0.68 0.87 1.64 1.97 1.78
PDCD6IP ENST00000457054 30.85 15.98 21.54 0.99 1.86 1.28 1.65 0.68 0.92
ZNF259 ENST00000227322 30.85 50.71 39.14 0.99 0.63 0.77 1.65 1.94 2.07
KIAA2022 ENST00000055682 30.86 6.08 16.27 0.99 2.78 1.70 1.65 0.35 0.66
PTPRF ENST00000359947 30.86 5.52 16.03 0.99 3.01 1.71 1.65 0.33 0.66

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