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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
TNS1 ENST00000171887 37.77 16.61 25.27 0.92 1.75 1.05 1.73 0.71 1.15
NGFR ENST00000172229 38.30 27.72 31.23 0.91 1.27 0.86 1.73 1.18 1.56
NTN1 ENST00000173229 32.37 2.58 15.24 0.99 3.54 1.83 1.70 0.29 0.65
ISOC1 ENST00000173527 57.77 76.09 68.98 0.57 0.43 0.46 1.55 0.86 1.04
TRO ENST00000173898 79.58 43.83 62.63 0.33 0.61 0.48 0.58 1.95 1.40
MNT ENST00000174618 39.01 3.87 19.44 0.90 3.30 1.53 1.76 0.31 0.84
LAPTM4A ENST00000175091 52.50 47.63 48.95 0.65 0.62 0.71 1.80 1.97 1.84
ADAM7 ENST00000175238 76.06 56.05 67.98 0.34 0.49 0.51 0.78 1.55 1.10
ASNS ENST00000175506 31.68 40.25 34.22 0.95 0.61 0.87 1.70 1.73 1.77
PTPN18 ENST00000175756 74.56 51.66 64.38 0.38 0.62 0.51 0.79 1.87 1.34
DRD4 ENST00000176183 85.56 93.12 92.05 0.28 0.28 0.14 0.46 0.30 0.16
SCT ENST00000176195 93.49 97.08 97.89 0.13 0.24 0.09 0.15 0.19 0.04
STK10 ENST00000176763 39.17 41.52 38.62 0.90 0.62 0.84 1.76 1.83 2.01
TBX21 ENST00000177694 26.28 7.50 14.64 1.33 2.52 1.97 1.27 0.40 0.59
CA12 ENST00000178638 46.79 71.17 59.16 0.56 0.52 0.49 1.80 1.06 1.68
MAP2K5 ENST00000178640 10.65 23.30 14.72 1.97 1.43 1.95 0.57 0.93 0.62
C12orf5 ENST00000179259 39.46 28.43 32.13 0.90 1.16 0.89 1.78 1.24 1.60
FGF20 ENST00000180166 59.62 27.81 41.96 0.57 1.23 0.68 1.41 1.19 2.01
MTMR7 ENST00000180173 60.61 53.10 56.67 0.58 0.66 0.52 1.34 1.77 1.71
CPB2 ENST00000181383 46.71 73.13 60.39 0.57 0.53 0.44 1.82 1.02 1.58
FAM107B ENST00000181796 66.50 76.20 74.21 0.59 0.43 0.39 1.03 0.85 0.69
CDK13 ENST00000181839 8.91 12.83 8.20 2.35 2.09 2.57 0.45 0.59 0.37
CRYBG3 ENST00000182096 42.18 23.07 30.85 0.78 1.46 0.77 1.74 0.91 1.49
TSPAN32 ENST00000182290 84.83 50.06 69.63 0.28 0.66 0.44 0.47 1.99 0.95
TRAM2 ENST00000182527 23.36 15.35 17.20 1.39 1.89 1.64 1.08 0.67 0.73

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