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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
BANF2 ENST00000545418 46.23 83.35 66.46 0.56 0.27 0.51 1.79 0.48 1.22
CPO ENST00000272852 46.24 88.61 69.62 0.56 0.24 0.44 1.79 0.35 0.95
CASP9 ENST00000333868 46.24 52.76 48.35 0.56 0.66 0.67 1.80 1.79 1.89
GPRASP2 ENST00000543253 46.25 10.80 26.64 0.56 2.11 0.99 1.80 0.51 1.25
HPX ENST00000265983 46.25 63.53 54.43 0.56 0.49 0.57 1.80 1.25 1.75
PLA2G15 ENST00000219345 46.26 26.59 34.65 0.56 1.19 0.90 1.80 1.12 1.76
HN1 ENST00000356033 46.26 69.23 57.74 0.56 0.56 0.49 1.80 1.13 1.67
CKMT1B ENST00000300283 46.27 74.43 60.97 0.56 0.53 0.43 1.79 1.00 1.58
NUP37 ENST00000552283 46.27 52.54 48.26 0.56 0.66 0.67 1.79 1.83 1.87
TBC1D9B ENST00000356834 46.28 34.91 38.92 0.56 0.76 0.80 1.79 1.54 2.06
KLF14 ENST00000310992 46.28 82.16 65.84 0.56 0.34 0.51 1.79 0.51 1.25
TMEM101 ENST00000589334 46.29 60.81 52.90 0.56 0.56 0.61 1.79 1.40 1.87
PTPN22 ENST00000359785 46.29 57.19 50.80 0.56 0.56 0.67 1.79 1.49 1.85
PPM1H ENST00000228705 46.30 18.72 30.77 0.56 1.52 0.78 1.79 0.74 1.49
PARP16 ENST00000261888 46.30 78.34 63.51 0.56 0.43 0.49 1.79 0.74 1.39
TOP3A ENST00000321105 46.31 36.05 39.52 0.56 0.81 0.80 1.79 1.58 2.03
PRSS37 ENST00000350549 46.31 71.45 59.03 0.56 0.53 0.48 1.78 1.05 1.66
OGN ENST00000262551 46.32 53.95 49.02 0.56 0.65 0.72 1.78 1.70 1.84
SH3BP5L ENST00000366472 46.33 34.25 38.57 0.56 0.85 0.84 1.78 1.56 2.01
IFFO1 ENST00000356896 46.33 36.99 40.01 0.56 0.76 0.82 1.78 1.68 1.99
DUSP22 ENST00000344450 46.34 45.46 44.39 0.56 0.70 0.61 1.78 1.99 2.03
ARRDC4 ENST00000268042 46.34 57.57 51.04 0.56 0.57 0.66 1.78 1.47 1.88
RNF115 ENST00000369291 46.35 42.37 42.65 0.56 0.59 0.68 1.78 1.90 2.02
SH3BP1 ENST00000357436 46.35 27.12 34.92 0.56 1.23 0.90 1.78 1.13 1.76
UBALD2 ENST00000327490 46.36 55.30 49.76 0.56 0.57 0.65 1.79 1.62 1.86

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