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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
PALB2 ENST00000261584 60.69 57.56 59.38 0.57 0.57 0.49 1.33 1.47 1.70
CRHR2 ENST00000348438 60.70 70.69 67.51 0.57 0.49 0.51 1.34 1.09 1.13
DSC3 ENST00000360428 60.70 68.61 66.36 0.57 0.53 0.53 1.34 1.18 1.20
FAM43A ENST00000329759 60.71 26.71 41.95 0.57 1.19 0.68 1.33 1.12 2.01
TLR2 ENST00000260010 60.71 55.02 57.90 0.57 0.57 0.48 1.33 1.63 1.66
COX7A1 ENST00000292907 60.72 93.33 80.33 0.57 0.28 0.38 1.33 0.29 0.52
SLC39A2 ENST00000298681 60.73 64.64 63.97 0.57 0.48 0.52 1.33 1.22 1.39
GGA3 ENST00000245541 60.73 37.79 48.12 0.57 0.80 0.66 1.33 1.70 1.87
RNASEH1 ENST00000315212 60.74 39.27 48.88 0.57 0.70 0.71 1.33 1.64 1.85
FFAR4 ENST00000371483 60.74 63.09 62.90 0.57 0.48 0.51 1.33 1.29 1.40
ZNF25 ENST00000302609 60.75 50.77 55.39 0.57 0.63 0.49 1.33 1.94 1.71
PCDHGA7 ENST00000518325 60.75 65.69 64.57 0.57 0.53 0.51 1.33 1.22 1.34
BARX2 ENST00000281437 60.76 36.16 47.21 0.57 0.82 0.67 1.33 1.60 1.89
SDC3 ENST00000339394 60.76 35.67 46.96 0.57 0.78 0.70 1.33 1.57 1.86
GRSF1 ENST00000254799 60.77 68.43 66.28 0.57 0.52 0.52 1.34 1.21 1.21
SPATA25 ENST00000372519 60.77 80.57 73.47 0.57 0.37 0.40 1.34 0.57 0.76
TCEAL3 ENST00000372628 60.78 37.04 47.73 0.57 0.77 0.65 1.34 1.68 1.88
ACP6 ENST00000369238 60.78 77.22 71.52 0.57 0.43 0.44 1.34 0.78 0.84
KIAA1919 ENST00000368847 60.79 64.94 64.14 0.57 0.48 0.52 1.34 1.24 1.37
TACC2 ENST00000369005 60.79 35.04 46.55 0.58 0.76 0.66 1.34 1.58 1.90
HTR3B ENST00000260191 60.80 50.73 55.39 0.58 0.63 0.49 1.34 1.94 1.71
SLC2A10 ENST00000359271 60.80 73.75 69.43 0.59 0.52 0.43 1.34 1.03 0.98
CXCR1 ENST00000295683 60.81 90.87 79.17 0.59 0.25 0.38 1.34 0.35 0.54
DCUN1D2 ENST00000478244 60.81 79.46 72.88 0.59 0.38 0.40 1.34 0.66 0.81
TRABD2B ENST00000606738 60.82 20.27 38.84 0.59 1.43 0.82 1.34 0.75 2.04

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