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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
GTF3C4 ENST00000372146 12.53 18.52 13.12 1.67 1.49 2.09 0.63 0.76 0.52
FBXO8 ENST00000393674 12.54 26.54 17.41 1.67 1.19 1.63 0.63 1.12 0.75
MYO5A ENST00000399231 12.54 11.21 9.33 1.67 2.09 2.32 0.63 0.54 0.38
LTA ENST00000454783 12.55 38.15 23.48 1.67 0.77 1.18 0.63 1.72 1.00
ARNT ENST00000358595 12.55 11.06 9.25 1.67 2.09 2.30 0.62 0.52 0.38
IDH3A ENST00000299518 12.56 28.58 18.52 1.67 1.16 1.62 0.62 1.27 0.81
CDK2AP1 ENST00000261692 12.56 46.25 27.52 1.67 0.73 0.96 0.63 2.04 1.27
LIN28A ENST00000326279 12.57 55.57 32.28 1.67 0.53 0.90 0.63 1.60 1.61
RNF17 ENST00000255324 12.57 0.83 4.01 1.67 4.08 3.76 0.63 0.28 0.23
PPME1 ENST00000328257 12.58 5.63 6.43 1.67 2.97 3.06 0.63 0.33 0.32
MEST ENST00000223215 12.58 23.14 15.69 1.67 1.46 1.77 0.64 0.90 0.67
GCM1 ENST00000259803 12.59 2.77 4.95 1.67 3.52 3.69 0.64 0.28 0.25
MYBL2 ENST00000217026 12.59 21.23 14.66 1.67 1.43 1.97 0.64 0.80 0.59
NAT8L ENST00000423729 12.60 23.26 15.76 1.67 1.43 1.77 0.64 0.92 0.66
SSH2 ENST00000269033 12.60 10.45 8.91 1.67 2.23 2.48 0.64 0.50 0.38
CPEB2 ENST00000538197 12.61 29.27 18.92 1.68 1.14 1.54 0.64 1.35 0.83
CRKL ENST00000354336 12.61 32.81 20.86 1.68 0.84 1.47 0.64 1.44 0.87
TPM4 ENST00000538887 12.62 27.54 17.99 1.68 1.25 1.70 0.64 1.17 0.78
PTGES ENST00000340607 12.62 46.88 27.90 1.68 0.71 0.85 0.64 1.95 1.29
LAMTOR1 ENST00000278671 12.63 29.00 18.82 1.68 1.15 1.57 0.64 1.31 0.83
GRK6 ENST00000528793 12.63 28.47 18.48 1.68 1.16 1.62 0.64 1.24 0.81
DOCK7 ENST00000340370 12.64 17.13 12.45 1.68 1.61 2.23 0.64 0.75 0.50
SYT14 ENST00000422431 12.64 14.54 11.26 1.68 2.04 2.16 0.64 0.61 0.45
SSB ENST00000409333 12.65 27.53 18.02 1.68 1.25 1.70 0.64 1.17 0.78
KANSL3 ENST00000431828 12.65 3.50 5.36 1.68 3.38 3.52 0.65 0.29 0.25

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