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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
C19orf33 ENST00000301246 82.90 45.19 65.62 0.30 0.70 0.51 0.55 1.98 1.29
HLA-DQB1 ENST00000374943 82.91 55.67 71.87 0.30 0.52 0.44 0.55 1.60 0.82
PARP9 ENST00000360356 82.91 43.67 64.65 0.30 0.62 0.51 0.55 1.97 1.32
TNFSF18 ENST00000404377 82.92 82.78 86.09 0.30 0.33 0.33 0.55 0.50 0.33
CYP2A6 ENST00000301141 82.92 65.71 77.52 0.30 0.53 0.35 0.55 1.22 0.57
CDT1 ENST00000301019 82.93 65.60 77.47 0.30 0.53 0.35 0.55 1.22 0.57
RPUSD1 ENST00000561734 82.93 93.16 91.01 0.30 0.28 0.15 0.55 0.30 0.20
CDC42EP1 ENST00000249014 82.94 87.13 88.19 0.30 0.22 0.23 0.55 0.41 0.30
MS4A5 ENST00000300190 82.95 78.86 84.17 0.30 0.40 0.34 0.55 0.71 0.42
AZI1 ENST00000450824 82.95 38.80 61.59 0.30 0.70 0.46 0.55 1.66 1.48
SLC25A6 ENST00000381401 82.96 41.58 63.43 0.30 0.63 0.49 0.55 1.80 1.37
HAVCR2 ENST00000307851 82.96 40.20 62.43 0.30 0.61 0.48 0.55 1.72 1.39
KRTAP20-2 ENST00000330798 82.97 98.76 93.76 0.30 0.16 0.10 0.55 0.14 0.13
MFSD3 ENST00000301327 82.97 90.26 89.72 0.30 0.25 0.18 0.55 0.38 0.23
TMEM80 ENST00000608174 82.98 96.71 92.60 0.30 0.23 0.14 0.55 0.19 0.15
IQCD ENST00000299732 82.98 91.73 90.38 0.30 0.24 0.15 0.55 0.32 0.21
OR5M8 ENST00000327216 82.99 73.25 81.46 0.29 0.54 0.35 0.55 1.02 0.48
OR5J2 ENST00000312298 82.99 87.79 88.51 0.29 0.24 0.22 0.55 0.37 0.28
FAM170B ENST00000311787 83.00 77.48 83.62 0.29 0.42 0.33 0.55 0.77 0.40
SPATA4 ENST00000280191 83.00 79.45 84.57 0.29 0.38 0.34 0.55 0.67 0.40
APCDD1L ENST00000371149 83.01 35.64 59.68 0.29 0.78 0.49 0.55 1.58 1.67
MAFA ENST00000333480 83.01 78.99 84.30 0.29 0.40 0.34 0.55 0.69 0.41
MAGEB18 ENST00000325250 83.02 91.72 90.41 0.29 0.24 0.15 0.55 0.32 0.21
PIDD ENST00000347755 83.02 58.43 73.52 0.28 0.54 0.40 0.55 1.38 0.74
MRPL23 ENST00000397298 83.03 96.10 92.25 0.28 0.21 0.14 0.55 0.20 0.16

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