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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
C1orf21 ENST00000235307 24.41 19.42 19.95 1.33 1.46 1.47 1.12 0.74 0.84
GLI3 ENST00000395925 24.42 5.24 12.41 1.33 3.14 2.23 1.12 0.32 0.50
ZNF687 ENST00000324048 24.42 11.19 15.64 1.33 2.09 1.75 1.12 0.54 0.67
USP14 ENST00000261601 24.43 15.24 17.75 1.33 1.89 1.67 1.12 0.67 0.78
NUMBL ENST00000252891 24.43 6.86 13.26 1.33 2.62 2.09 1.12 0.37 0.54
ITGA5 ENST00000293379 24.44 15.46 17.87 1.33 1.87 1.68 1.12 0.67 0.77
PKD2 ENST00000237596 24.44 24.68 22.72 1.33 1.29 1.18 1.12 1.04 0.98
CD40LG ENST00000370629 24.45 28.52 24.55 1.34 1.15 1.06 1.12 1.26 1.09
SASH3 ENST00000356892 24.45 34.48 27.60 1.35 0.80 0.97 1.12 1.56 1.26
CHSY1 ENST00000254190 24.46 16.30 18.30 1.35 1.78 1.66 1.12 0.70 0.79
MNAT1 ENST00000261245 24.46 81.12 51.99 1.34 0.35 0.62 1.12 0.55 1.93
GNS ENST00000258145 24.47 31.70 26.24 1.34 0.95 1.01 1.12 1.46 1.26
VPS72 ENST00000354473 24.47 47.36 34.10 1.34 0.66 0.91 1.12 2.01 1.74
WSCD2 ENST00000332082 24.48 18.21 19.37 1.34 1.49 1.54 1.12 0.74 0.85
SGIP1 ENST00000371037 24.48 5.88 12.75 1.34 2.83 2.14 1.12 0.35 0.52
RB1CC1 ENST00000025008 24.49 2.56 11.17 1.34 3.55 2.18 1.12 0.29 0.45
ASS1 ENST00000372394 24.49 53.23 37.10 1.34 0.66 0.80 1.12 1.75 1.95
C7orf43 ENST00000316937 24.50 26.16 23.42 1.34 1.19 1.19 1.12 1.08 1.01
AHCY ENST00000217426 24.50 32.83 26.82 1.34 0.85 0.96 1.12 1.44 1.28
PHF14 ENST00000403050 24.51 19.93 20.29 1.34 1.46 1.47 1.12 0.73 0.89
UBE2J1 ENST00000435041 24.51 20.10 20.41 1.34 1.43 1.51 1.12 0.74 0.88
DST ENST00000244364 24.52 3.88 11.81 1.34 3.29 2.21 1.12 0.31 0.46
DPM1 ENST00000371588 24.52 46.29 33.56 1.34 0.73 0.87 1.12 2.04 1.72
RAP1GDS1 ENST00000339360 24.53 15.37 17.86 1.34 1.90 1.66 1.12 0.68 0.77
ATG4A ENST00000372232 24.53 9.95 15.06 1.34 2.32 1.87 1.12 0.50 0.63

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