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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
PSMB7 ENST00000259457 19.63 18.95 17.15 1.56 1.52 1.64 1.01 0.75 0.73
GIT2 ENST00000355312 19.64 10.23 12.50 1.56 2.29 2.21 1.01 0.49 0.50
BCL2 ENST00000398117 19.64 37.36 26.66 1.56 0.76 0.99 1.01 1.65 1.25
EXTL3 ENST00000220562 19.65 33.85 24.79 1.56 0.84 1.04 1.01 1.56 1.10
SMIM11 ENST00000399295 19.65 52.06 34.06 1.56 0.59 0.91 1.01 1.85 1.73
KLHL9 ENST00000359039 19.66 20.51 17.99 1.56 1.43 1.70 1.01 0.78 0.78
SLC30A9 ENST00000264451 19.66 32.29 24.02 1.56 0.86 1.10 1.01 1.46 1.05
HOXB1 ENST00000239174 19.67 37.82 26.92 1.56 0.80 0.99 1.00 1.70 1.27
VWC2 ENST00000340652 19.67 10.38 12.57 1.56 2.25 2.21 1.00 0.50 0.52
TRPM7 ENST00000313478 19.68 28.32 22.11 1.54 1.16 1.15 1.00 1.22 0.97
SNX14 ENST00000314673 19.68 44.34 30.18 1.54 0.61 0.81 1.00 1.95 1.45
LPHN3 ENST00000514591 19.69 5.00 9.88 1.54 3.25 2.30 1.00 0.32 0.41
SEC14L1 ENST00000392476 19.69 15.49 15.36 1.54 1.87 1.80 1.00 0.67 0.66
FOXF2 ENST00000259806 19.70 21.45 18.53 1.54 1.43 1.62 1.00 0.80 0.81
SPCS2 ENST00000263672 19.70 17.39 16.35 1.54 1.59 1.71 1.00 0.74 0.67
MFF ENST00000353339 19.71 29.90 22.95 1.54 1.13 1.19 1.00 1.41 0.98
FGR ENST00000374005 19.71 20.49 18.04 1.54 1.43 1.70 1.00 0.78 0.78
CAMTA2 ENST00000414043 19.72 10.34 12.58 1.54 2.25 2.20 1.00 0.50 0.52
RPL10A ENST00000322203 19.73 21.65 18.69 1.54 1.46 1.57 1.00 0.81 0.81
FRYL ENST00000358350 19.73 10.36 12.60 1.56 2.24 2.20 1.00 0.50 0.52
SLC25A27 ENST00000371347 19.74 37.60 26.83 1.56 0.80 0.97 1.00 1.68 1.28
IDE ENST00000265986 19.74 19.13 17.31 1.56 1.49 1.63 1.00 0.76 0.74
TEK ENST00000380036 19.75 4.63 9.67 1.54 3.26 2.26 1.00 0.31 0.40
MZT1 ENST00000377818 19.75 86.26 52.25 1.54 0.25 0.59 1.00 0.42 1.90
BMP10 ENST00000295379 19.76 19.54 17.51 1.54 1.43 1.63 1.00 0.74 0.75

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