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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
SDF4 ENST00000360001 57.72 40.19 47.81 0.57 0.61 0.65 1.55 1.72 1.89
ECI2 ENST00000380118 57.73 67.68 63.98 0.57 0.53 0.52 1.55 1.19 1.38
P2RX6 ENST00000413302 57.73 62.76 60.86 0.57 0.51 0.43 1.55 1.31 1.60
TRMT61A ENST00000389749 57.74 57.93 57.83 0.57 0.57 0.51 1.55 1.46 1.66
FAM221A ENST00000344962 57.74 84.80 74.12 0.57 0.27 0.39 1.55 0.42 0.69
UPK1B ENST00000264234 57.75 72.63 66.90 0.57 0.47 0.53 1.55 1.04 1.20
SP6 ENST00000536300 57.76 40.87 48.19 0.57 0.61 0.66 1.55 1.78 1.87
DNAI2 ENST00000446837 57.76 55.05 56.14 0.57 0.58 0.49 1.55 1.63 1.77
DNAJC22 ENST00000549441 57.77 80.01 71.37 0.57 0.37 0.43 1.55 0.61 0.86
ISOC1 ENST00000173527 57.77 76.09 68.98 0.57 0.43 0.46 1.55 0.86 1.04
RGS18 ENST00000367460 57.78 62.90 60.94 0.57 0.51 0.43 1.55 1.31 1.58
UCP1 ENST00000262999 57.78 88.56 76.23 0.57 0.24 0.37 1.55 0.36 0.62
TNS3 ENST00000398879 57.79 3.89 29.01 0.57 3.29 0.82 1.55 0.31 1.31
SPNS2 ENST00000329078 57.79 43.39 49.55 0.57 0.61 0.67 1.55 1.95 1.85
SNX3 ENST00000230085 57.80 33.67 44.21 0.57 0.84 0.62 1.54 1.55 2.04
UBL4A ENST00000369660 57.80 64.09 61.68 0.57 0.49 0.46 1.54 1.20 1.46
ARPC1B ENST00000451682 57.81 35.75 45.48 0.57 0.78 0.70 1.54 1.58 1.97
CTDP1 ENST00000299543 57.81 25.26 39.88 0.57 1.29 0.78 1.54 1.02 2.02
METTL4 ENST00000574538 57.82 48.58 52.51 0.57 0.65 0.61 1.54 2.01 1.90
SVIL ENST00000375398 57.82 16.86 35.50 0.57 1.66 0.86 1.54 0.71 1.77
IMMT ENST00000410111 57.83 21.97 38.22 0.57 1.47 0.85 1.54 0.81 2.05
TVP23B ENST00000307767 57.83 53.64 55.37 0.57 0.63 0.49 1.54 1.70 1.72
PIH1D3 ENST00000535523 57.84 23.96 39.28 0.57 1.38 0.80 1.54 0.95 2.04
CHRNB3 ENST00000289957 57.84 57.33 57.55 0.57 0.54 0.51 1.54 1.49 1.66
EXOSC7 ENST00000265564 57.85 60.83 59.65 0.57 0.56 0.49 1.54 1.41 1.67

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