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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
PFKL ENST00000349048 40.55 53.91 45.93 0.86 0.65 0.70 1.76 1.70 1.97
RP11-644F5.10 ENST00000550412 40.56 60.79 49.60 0.86 0.56 0.67 1.75 1.39 1.84
FAM65B ENST00000259698 40.56 13.09 24.87 0.86 2.06 1.02 1.75 0.59 1.10
CALR3 ENST00000269881 40.57 65.39 52.22 0.86 0.53 0.61 1.75 1.25 1.90
GPR65 ENST00000267549 40.57 43.90 40.48 0.86 0.61 0.80 1.75 1.96 2.04
PAGR1 ENST00000609618 40.58 27.33 32.16 0.86 1.27 0.91 1.75 1.16 1.59
PAGR1 ENST00000320330 40.58 27.36 32.19 0.86 1.25 0.91 1.75 1.17 1.60
TRIM54 ENST00000296098 40.59 85.48 64.31 0.86 0.25 0.51 1.75 0.45 1.36
LRRFIP2 ENST00000421307 40.59 53.62 45.82 0.86 0.62 0.68 1.75 1.72 1.97
HOXB5 ENST00000239151 40.60 30.02 33.46 0.86 1.09 0.89 1.75 1.43 1.72
CHST10 ENST00000264249 40.60 52.24 45.04 0.86 0.62 0.70 1.75 1.84 2.03
EXOSC8 ENST00000389704 40.61 84.44 63.76 0.86 0.29 0.49 1.75 0.44 1.38
PNPT1 ENST00000447944 40.61 22.93 29.95 0.86 1.47 0.86 1.75 0.90 1.46
SLC5A12 ENST00000396005 40.62 34.53 35.70 0.86 0.80 0.84 1.75 1.55 1.77
GPR143 ENST00000467482 40.62 16.54 26.75 0.86 1.78 0.97 1.75 0.69 1.27
DOCK10 ENST00000258390 40.63 18.09 27.47 0.86 1.53 0.96 1.75 0.74 1.27
AASDHPPT ENST00000278618 40.63 37.42 37.32 0.86 0.75 0.84 1.75 1.66 2.02
PCP4L1 ENST00000504449 40.64 84.04 63.52 0.86 0.27 0.49 1.75 0.45 1.39
LRRC17 ENST00000339431 40.64 68.66 54.17 0.86 0.53 0.61 1.75 1.17 1.74
PIGH ENST00000216452 40.65 48.51 42.89 0.86 0.65 0.67 1.75 2.02 1.99
THSD7A ENST00000423059 40.65 6.69 21.81 0.86 2.66 1.23 1.75 0.37 0.94
AC004381.6 ENST00000261377 40.66 41.63 39.51 0.86 0.62 0.80 1.75 1.80 2.03
OR6B1 ENST00000408922 40.66 87.02 65.37 0.86 0.22 0.53 1.75 0.40 1.31
PPARGC1B ENST00000309241 40.67 16.72 26.86 0.86 1.68 0.97 1.75 0.71 1.27
PKLR ENST00000342741 40.67 48.59 43.00 0.86 0.65 0.67 1.74 2.01 2.01

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