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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
DNASE1L3 ENST00000318316 65.21 61.52 64.75 0.54 0.54 0.49 1.15 1.40 1.32
TCHP ENST00000312777 65.22 55.40 60.92 0.54 0.58 0.43 1.15 1.60 1.58
VRK2 ENST00000435505 65.22 58.01 62.48 0.54 0.53 0.48 1.14 1.44 1.40
KRT7 ENST00000331817 65.23 77.78 74.41 0.54 0.42 0.40 1.14 0.79 0.70
PTGDR ENST00000306051 65.23 78.24 74.66 0.54 0.43 0.40 1.14 0.74 0.68
SPSB3 ENST00000566339 65.24 36.08 49.59 0.54 0.81 0.67 1.14 1.59 1.84
ZFP37 ENST00000374227 65.24 74.69 72.65 0.54 0.54 0.43 1.14 0.96 0.81
GTF2F1 ENST00000394456 65.25 34.58 48.81 0.54 0.80 0.70 1.14 1.54 1.86
FOXQ1 ENST00000296839 65.25 53.07 59.42 0.56 0.66 0.49 1.14 1.78 1.71
APH1B ENST00000261879 65.26 85.53 78.65 0.56 0.27 0.38 1.14 0.44 0.55
CDC42EP4 ENST00000335793 65.27 47.85 56.39 0.56 0.59 0.51 1.14 1.98 1.73
GPR39 ENST00000329321 65.27 90.30 81.11 0.56 0.25 0.39 1.14 0.38 0.49
BATF2 ENST00000301887 65.28 57.49 62.16 0.56 0.56 0.48 1.14 1.48 1.44
C11orf85 ENST00000301896 65.28 62.00 65.08 0.56 0.56 0.51 1.14 1.37 1.31
C4orf17 ENST00000326581 65.29 77.13 74.01 0.56 0.42 0.39 1.14 0.78 0.70
MMD2 ENST00000404774 65.29 74.46 72.55 0.56 0.53 0.46 1.13 0.99 0.82
MTHFD2L ENST00000395759 65.30 64.86 66.81 0.56 0.48 0.53 1.14 1.24 1.20
TST ENST00000403892 65.30 80.43 75.88 0.56 0.37 0.38 1.14 0.59 0.63
OPRD1 ENST00000234961 65.31 69.00 69.26 0.56 0.54 0.43 1.13 1.15 0.98
RMDN1 ENST00000406452 65.31 68.51 68.94 0.56 0.52 0.46 1.13 1.20 1.04
BRI3 ENST00000297290 65.32 90.83 81.43 0.56 0.25 0.35 1.14 0.35 0.48
GJA10 ENST00000369352 65.32 75.85 73.36 0.56 0.43 0.43 1.13 0.88 0.78
THEMIS2 ENST00000373921 65.33 39.10 51.31 0.56 0.70 0.63 1.12 1.63 1.91
C1orf109 ENST00000358011 65.33 75.70 73.30 0.56 0.44 0.43 1.12 0.88 0.79
DHRS9 ENST00000327239 65.34 83.77 77.75 0.56 0.28 0.38 1.12 0.47 0.55

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