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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
RPS6KB2 ENST00000312629 65.47 76.83 73.94 0.56 0.42 0.40 1.10 0.81 0.69
KIF24 ENST00000379166 65.48 48.48 56.83 0.56 0.65 0.52 1.10 2.02 1.69
CD164 ENST00000310786 65.48 31.47 47.24 0.57 0.96 0.67 1.10 1.43 1.88
SULT1C2 ENST00000326853 65.49 73.39 72.04 0.57 0.54 0.43 1.10 1.03 0.81
RASL10A ENST00000216101 65.49 58.35 62.92 0.57 0.54 0.51 1.10 1.41 1.40
AACS ENST00000316519 65.50 60.35 64.21 0.57 0.53 0.51 1.10 1.41 1.35
DHRS13 ENST00000378895 65.50 51.03 58.31 0.57 0.65 0.49 1.09 1.92 1.64
IRF3 ENST00000601291 65.51 48.24 56.68 0.57 0.63 0.52 1.09 2.00 1.71
IL17RD ENST00000296318 65.51 34.24 48.75 0.57 0.84 0.68 1.09 1.56 1.85
PIM3 ENST00000360612 65.52 8.70 35.33 0.57 2.47 0.87 1.10 0.48 1.76
RXFP4 ENST00000368318 65.52 85.43 78.73 0.57 0.25 0.38 1.10 0.45 0.54
MRPL9 ENST00000368830 65.53 51.67 58.71 0.57 0.61 0.52 1.10 1.87 1.65
CRYGB ENST00000260988 65.53 90.49 81.37 0.57 0.25 0.38 1.10 0.37 0.49
C7orf10 ENST00000309930 65.54 57.00 62.04 0.57 0.56 0.48 1.10 1.52 1.44
CCL20 ENST00000358813 65.54 92.17 82.24 0.57 0.25 0.35 1.09 0.31 0.44
NT5C ENST00000245552 65.55 70.24 70.11 0.57 0.52 0.46 1.09 1.12 0.90
TTC1 ENST00000231238 65.55 57.78 62.55 0.57 0.57 0.48 1.09 1.47 1.40
CXCL10 ENST00000306602 65.56 53.29 59.77 0.57 0.66 0.49 1.09 1.71 1.65
NDUFC2 ENST00000281031 65.56 42.45 53.42 0.57 0.59 0.62 1.09 1.89 1.84
ACOT8 ENST00000217455 65.57 54.49 60.56 0.57 0.59 0.44 1.09 1.66 1.58
C9orf69 ENST00000418388 65.58 79.20 75.30 0.58 0.39 0.37 1.09 0.69 0.66
PCDHA6 ENST00000529310 65.58 60.81 64.53 0.58 0.56 0.51 1.09 1.40 1.34
IL13RA2 ENST00000371936 65.59 65.55 67.34 0.58 0.53 0.52 1.09 1.22 1.15
RRP1 ENST00000497547 65.59 41.20 52.70 0.58 0.59 0.61 1.09 1.83 1.89
SPINT1 ENST00000344051 65.60 44.65 54.71 0.58 0.66 0.57 1.09 1.97 1.73

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