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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
ANAPC11 ENST00000357385 68.70 38.16 52.75 0.56 0.77 0.61 0.95 1.72 1.88
TRMU ENST00000290846 68.71 81.91 78.55 0.56 0.35 0.38 0.95 0.51 0.55
AC005609.1 ENST00000502505 68.71 88.45 81.97 0.56 0.23 0.37 0.95 0.37 0.47
CNGB1 ENST00000251102 68.72 63.05 67.74 0.56 0.48 0.52 0.95 1.31 1.12
FAM161A ENST00000404929 68.72 57.56 64.43 0.56 0.57 0.51 0.95 1.47 1.34
MTX3 ENST00000512560 68.73 59.46 65.72 0.56 0.51 0.51 0.95 1.41 1.26
MC5R ENST00000324750 68.73 90.88 83.18 0.56 0.25 0.29 0.95 0.35 0.40
RSPO4 ENST00000217260 68.74 82.90 79.14 0.56 0.32 0.39 0.95 0.49 0.54
DNAJB8 ENST00000469083 68.74 72.34 73.32 0.56 0.51 0.43 0.95 1.03 0.78
CCDC60 ENST00000327554 68.75 52.34 61.17 0.56 0.62 0.43 0.95 1.81 1.51
OR51B6 ENST00000380219 68.75 94.01 84.74 0.56 0.25 0.34 0.95 0.26 0.40
STARD8 ENST00000374599 68.76 24.33 45.22 0.56 1.33 0.70 0.95 1.00 2.00
CCDC96 ENST00000310085 68.76 86.33 80.86 0.56 0.25 0.39 0.95 0.43 0.51
EMP1 ENST00000256951 68.77 42.85 55.47 0.56 0.62 0.51 0.95 1.92 1.73
USP35 ENST00000529308 68.77 38.54 53.08 0.56 0.73 0.62 0.95 1.67 1.87
TRIM25 ENST00000316881 68.78 30.48 48.47 0.56 1.09 0.68 0.95 1.38 1.86
TMEM45B ENST00000281441 68.78 91.61 83.56 0.56 0.23 0.33 0.95 0.32 0.40
SECISBP2 ENST00000375807 68.79 56.78 64.05 0.56 0.53 0.52 0.95 1.55 1.39
VIPR1 ENST00000325123 68.79 85.14 80.28 0.56 0.25 0.38 0.95 0.45 0.51
CST6 ENST00000312134 68.80 54.15 62.31 0.56 0.63 0.49 0.95 1.68 1.41
ARMC7 ENST00000245543 68.80 66.12 69.68 0.56 0.53 0.44 0.95 1.20 0.95
MMACHC ENST00000401061 68.81 86.44 80.97 0.56 0.24 0.39 0.95 0.42 0.50
CRYBA2 ENST00000295728 68.81 72.47 73.45 0.56 0.47 0.40 0.95 1.03 0.76
SLC13A2 ENST00000444914 68.82 63.95 68.35 0.56 0.48 0.49 0.95 1.21 1.07
TRPT1 ENST00000394546 68.82 54.54 62.56 0.56 0.59 0.48 0.95 1.65 1.40

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