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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
LONRF1 ENST00000398246 37.58 17.93 25.91 0.92 1.53 1.01 1.76 0.73 1.23
GBA ENST00000327247 37.59 41.58 37.80 0.92 0.63 0.84 1.76 1.80 2.01
CSPP1 ENST00000262210 37.59 46.78 40.45 0.92 0.72 0.80 1.76 1.97 2.02
RNF44 ENST00000274811 37.60 25.49 29.70 0.92 1.25 0.86 1.76 1.06 1.41
MAN2A1 ENST00000261483 37.60 31.93 32.94 0.92 0.94 0.86 1.76 1.48 1.67
TMEM68 ENST00000334667 37.61 54.16 44.38 0.92 0.63 0.62 1.76 1.69 2.03
EEF1E1 ENST00000379715 37.61 51.16 42.68 0.92 0.66 0.68 1.76 1.90 2.02
CHST2 ENST00000309575 37.62 43.51 38.89 0.92 0.59 0.80 1.76 1.97 2.06
NKIRAS1 ENST00000443659 37.62 72.70 54.75 0.92 0.47 0.56 1.76 1.03 1.73
PARD6G ENST00000353265 37.63 48.39 41.22 0.94 0.63 0.76 1.76 2.00 2.01
RHBDL2 ENST00000289248 37.63 73.79 55.35 0.94 0.53 0.49 1.76 1.02 1.73
PGAP1 ENST00000354764 37.64 30.65 32.34 0.92 1.05 0.90 1.76 1.38 1.61
CTSD ENST00000236671 37.64 41.31 37.71 0.92 0.62 0.84 1.75 1.82 2.01
KIAA1199 ENST00000394685 37.65 38.26 36.07 0.92 0.75 0.87 1.75 1.70 1.79
MPL ENST00000372470 37.65 41.25 37.68 0.92 0.61 0.82 1.75 1.83 2.01
SVIP ENST00000354193 37.66 87.92 64.06 0.92 0.25 0.52 1.75 0.37 1.37
SPATA16 ENST00000351008 37.66 58.07 46.52 0.92 0.53 0.66 1.75 1.46 1.90
CA11 ENST00000084798 37.67 42.06 38.15 0.92 0.61 0.86 1.75 1.85 2.04
MECP2 ENST00000453960 37.67 25.52 29.81 0.94 1.25 0.85 1.75 1.06 1.43
FNDC7 ENST00000370017 37.68 53.33 43.88 0.94 0.66 0.62 1.75 1.70 2.02
TMTC1 ENST00000539277 37.68 38.44 36.14 0.94 0.75 0.87 1.75 1.70 1.79
PITHD1 ENST00000246151 37.69 54.21 44.48 0.94 0.62 0.61 1.75 1.70 2.04
BMS1 ENST00000374518 37.69 20.79 27.35 0.94 1.44 0.97 1.74 0.81 1.25
LONRF3 ENST00000371628 37.70 18.84 26.37 0.94 1.53 1.01 1.74 0.74 1.25
ACPL2 ENST00000286353 37.70 40.64 37.41 0.94 0.63 0.85 1.74 1.77 2.00

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