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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
PMP22 ENST00000395938 26.73 17.42 20.15 1.30 1.59 1.49 1.34 0.73 0.87
FAM20B ENST00000263733 26.74 49.06 36.01 1.30 0.67 0.87 1.35 2.03 1.79
PBDC1 ENST00000373358 26.74 42.22 32.68 1.30 0.61 0.86 1.35 1.88 1.63
ARHGAP17 ENST00000289968 26.75 22.30 22.70 1.30 1.52 1.18 1.35 0.82 0.97
ILK ENST00000396751 26.75 41.02 32.07 1.30 0.59 0.90 1.35 1.80 1.60
TMEFF1 ENST00000374879 26.76 23.01 23.03 1.30 1.44 1.21 1.36 0.91 0.98
GALNT16 ENST00000337827 26.77 31.20 27.15 1.30 1.00 0.99 1.36 1.36 1.25
IQCB1 ENST00000310864 26.77 49.31 36.16 1.30 0.65 0.87 1.37 2.02 1.80
TMCC3 ENST00000261226 26.78 53.73 38.54 1.30 0.63 0.84 1.37 1.70 2.02
OSTC ENST00000512478 26.78 57.25 40.28 1.30 0.56 0.80 1.37 1.49 1.99
SMIM12 ENST00000521580 26.79 65.62 44.83 1.30 0.53 0.66 1.37 1.21 2.04
ABHD17A ENST00000250974 26.79 42.23 32.69 1.30 0.61 0.86 1.37 1.89 1.63
RNPEPL1 ENST00000270357 26.80 41.36 32.28 1.30 0.62 0.90 1.37 1.82 1.61
PPP2R4 ENST00000393370 26.80 9.38 15.93 1.32 2.49 1.76 1.36 0.49 0.66
ZNF746 ENST00000458143 26.81 19.53 21.25 1.30 1.43 1.40 1.36 0.74 0.90
DEPDC7 ENST00000241051 26.81 60.41 41.83 1.32 0.53 0.70 1.36 1.41 2.02
WNT8A ENST00000398754 26.82 40.10 31.66 1.32 0.63 0.89 1.35 1.71 1.58
WDR75 ENST00000314761 26.82 26.06 24.51 1.32 1.20 1.08 1.36 1.10 1.08
CEP170 ENST00000366542 26.83 4.16 13.11 1.33 3.25 2.10 1.36 0.32 0.52
C18orf8 ENST00000269221 26.83 13.54 18.13 1.33 2.06 1.67 1.36 0.61 0.79
DLK2 ENST00000357338 26.84 23.60 23.34 1.32 1.39 1.20 1.36 0.93 0.98
PRKCZ ENST00000378567 26.84 18.36 20.72 1.32 1.48 1.47 1.36 0.75 0.88
EBNA1BP2 ENST00000431635 26.85 60.29 41.80 1.32 0.53 0.72 1.36 1.39 2.01
BAG4 ENST00000287322 26.85 39.43 31.38 1.32 0.70 0.87 1.36 1.64 1.55
FAM208A ENST00000493960 26.86 9.64 16.07 1.32 2.45 1.70 1.36 0.50 0.66

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