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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
ANKK1 ENST00000303941 40.81 65.84 52.64 0.86 0.54 0.59 1.75 1.22 1.89
CWC22 ENST00000410053 40.81 24.15 30.74 0.86 1.34 0.78 1.75 0.99 1.48
LRFN4 ENST00000309602 40.82 19.35 28.25 0.85 1.49 0.80 1.75 0.75 1.29
MYOZ1 ENST00000359322 40.82 70.86 55.50 0.85 0.49 0.51 1.74 1.07 1.74
CAPN2 ENST00000295006 40.83 57.12 47.83 0.84 0.56 0.65 1.74 1.50 1.89
LIMD1 ENST00000273317 40.83 21.07 29.11 0.84 1.44 0.84 1.75 0.82 1.32
DUSP19 ENST00000354221 40.84 69.40 54.72 0.84 0.56 0.56 1.75 1.14 1.73
FSD1 ENST00000221856 40.84 23.30 30.26 0.84 1.43 0.84 1.75 0.93 1.44
MARCH2 ENST00000602117 40.85 47.55 42.46 0.84 0.61 0.68 1.74 2.02 2.01
TRAF5 ENST00000261464 40.86 61.39 50.13 0.84 0.54 0.62 1.74 1.40 1.90
IMPA2 ENST00000269159 40.86 50.28 43.97 0.84 0.67 0.61 1.74 1.97 2.02
GDF2 ENST00000249598 40.87 53.85 46.07 0.84 0.63 0.68 1.73 1.70 1.97
FAM102A ENST00000373095 40.87 25.77 31.51 0.84 1.23 0.86 1.73 1.05 1.57
SEMA4G ENST00000210633 40.88 41.69 39.64 0.84 0.61 0.80 1.73 1.80 2.04
NRG3 ENST00000372141 40.88 23.21 30.24 0.84 1.43 0.82 1.73 0.92 1.44
PGS1 ENST00000262764 40.89 63.47 51.28 0.84 0.49 0.63 1.73 1.25 1.92
TM2D2 ENST00000456397 40.89 50.56 44.18 0.84 0.63 0.62 1.73 1.95 2.05
BTBD1 ENST00000261721 40.90 44.51 40.89 0.84 0.63 0.78 1.72 1.98 2.06
C18orf21 ENST00000592875 40.90 80.23 61.24 0.84 0.37 0.43 1.72 0.58 1.49
DTNB ENST00000406818 40.91 40.40 38.99 0.84 0.61 0.80 1.72 1.76 2.06
SCP2D1 ENST00000377428 40.91 91.79 68.32 0.84 0.23 0.49 1.72 0.32 1.07
SERINC3 ENST00000342374 40.92 19.63 28.44 0.84 1.43 0.78 1.72 0.74 1.30
TMEM8B ENST00000377988 40.92 49.90 43.78 0.84 0.66 0.61 1.72 2.02 2.01
C5orf22 ENST00000325366 40.93 40.17 38.87 0.84 0.61 0.80 1.72 1.72 2.05
PLCXD2 ENST00000477665 40.93 76.64 58.90 0.84 0.42 0.49 1.72 0.83 1.65

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