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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
CSTL1 ENST00000347397 84.20 94.89 92.24 0.32 0.23 0.14 0.47 0.23 0.16
FAM35A ENST00000298784 84.20 43.30 65.21 0.32 0.61 0.53 0.47 1.93 1.29
ACTR3C ENST00000539352 84.21 76.10 83.51 0.30 0.43 0.33 0.47 0.86 0.40
PTX4 ENST00000293922 84.21 85.47 87.99 0.30 0.25 0.24 0.47 0.45 0.31
CDPF1 ENST00000314567 84.22 95.70 92.71 0.30 0.23 0.14 0.47 0.20 0.15
NUDT19 ENST00000397061 84.22 97.25 93.48 0.30 0.23 0.11 0.47 0.19 0.15
MT1H ENST00000332374 84.23 92.23 91.17 0.30 0.25 0.15 0.47 0.31 0.18
APITD1 ENST00000602787 84.23 87.54 89.00 0.30 0.23 0.19 0.47 0.37 0.27
APITD1-CORT ENST00000400900 84.24 87.54 89.00 0.30 0.23 0.19 0.47 0.37 0.27
SULT1A1 ENST00000395609 84.24 84.09 87.36 0.30 0.27 0.28 0.47 0.45 0.31
CRELD2 ENST00000404488 84.25 58.98 74.53 0.30 0.52 0.40 0.47 1.42 0.69
FCN2 ENST00000291744 84.25 81.51 86.12 0.30 0.33 0.33 0.47 0.53 0.33
C19orf55 ENST00000544099 84.26 59.80 74.95 0.30 0.52 0.40 0.47 1.37 0.64
DCAF8L1 ENST00000441525 84.26 99.28 94.56 0.30 0.15 0.09 0.47 0.12 0.11
LRP5L ENST00000402859 84.27 89.66 90.02 0.30 0.27 0.18 0.46 0.36 0.22
OCSTAMP ENST00000279028 84.27 70.07 80.50 0.30 0.53 0.39 0.46 1.14 0.51
GSTA1 ENST00000334575 84.28 83.61 87.12 0.30 0.27 0.28 0.46 0.47 0.30
YIPF7 ENST00000332990 84.28 74.35 82.73 0.30 0.53 0.32 0.46 1.00 0.42
ZNF607 ENST00000355202 84.29 53.58 71.45 0.30 0.62 0.46 0.46 1.70 0.86
FCRL4 ENST00000271532 84.29 52.03 70.48 0.30 0.61 0.43 0.47 1.86 0.91
APCS ENST00000255040 84.30 91.35 90.88 0.30 0.23 0.15 0.47 0.34 0.20
CHRFAM7A ENST00000299847 84.30 62.18 76.34 0.30 0.52 0.35 0.47 1.35 0.61
H3F3A ENST00000366813 84.31 63.98 77.32 0.30 0.48 0.35 0.47 1.20 0.58
SYNM ENST00000336292 84.31 62.16 76.33 0.30 0.53 0.35 0.47 1.35 0.61
OR5B2 ENST00000302581 84.32 77.88 84.44 0.30 0.42 0.33 0.47 0.79 0.40

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