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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
EFNA3 ENST00000505139 49.59 31.64 38.94 0.54 0.95 0.80 1.82 1.44 2.06
MAPK4 ENST00000400384 49.59 27.04 36.41 0.54 1.23 0.84 1.83 1.12 1.87
GRK7 ENST00000264952 49.60 66.10 57.87 0.54 0.54 0.48 1.83 1.20 1.66
TMEM144 ENST00000296529 49.60 75.48 63.79 0.54 0.44 0.49 1.83 0.90 1.38
RPS6KA4 ENST00000334205 49.61 10.47 28.22 0.54 2.23 0.81 1.84 0.50 1.29
OPN3 ENST00000366554 49.62 52.64 50.15 0.54 0.68 0.63 1.84 1.81 1.90
FGD2 ENST00000274963 49.62 42.03 44.30 0.54 0.59 0.61 1.84 1.84 2.04
RCBTB2 ENST00000344532 49.63 52.23 49.88 0.54 0.62 0.63 1.84 1.84 1.89
BRDT ENST00000362005 49.63 34.57 40.36 0.54 0.80 0.80 1.85 1.54 2.02
DENND6B ENST00000413817 49.64 43.65 45.33 0.54 0.62 0.70 1.84 1.97 2.00
TRABD ENST00000303434 49.64 37.25 41.67 0.54 0.76 0.72 1.85 1.66 2.01
SERTAD1 ENST00000357949 49.65 62.33 55.67 0.54 0.53 0.53 1.85 1.33 1.73
S100A4 ENST00000368716 49.65 91.63 73.45 0.54 0.23 0.40 1.85 0.32 0.76
HMGN2 ENST00000361427 49.66 22.31 34.23 0.54 1.52 0.86 1.85 0.82 1.76
PCDHGA4 ENST00000571252 49.66 65.36 57.44 0.54 0.53 0.51 1.85 1.25 1.66
EGF ENST00000265171 49.67 38.88 42.54 0.54 0.70 0.68 1.85 1.65 2.02
C5orf51 ENST00000381647 49.67 52.07 49.86 0.54 0.59 0.65 1.84 1.85 1.89
HS6ST2 ENST00000521489 49.68 52.52 50.09 0.54 0.66 0.62 1.84 1.83 1.92
SLC44A3 ENST00000271227 49.68 78.49 65.69 0.54 0.42 0.51 1.84 0.74 1.27
FAM168B ENST00000409185 49.69 63.45 56.36 0.54 0.49 0.49 1.84 1.26 1.74
PTPN13 ENST00000436978 49.69 31.88 39.14 0.54 0.94 0.77 1.84 1.48 2.07
FABP3 ENST00000373713 49.70 51.59 49.58 0.54 0.62 0.67 1.85 1.87 1.84
DDX49 ENST00000247003 49.70 66.87 58.34 0.54 0.53 0.49 1.85 1.24 1.65
MAP7D2 ENST00000379643 49.71 22.32 34.29 0.54 1.52 0.87 1.84 0.82 1.76
FYTTD1 ENST00000241502 49.71 27.13 36.52 0.54 1.23 0.85 1.84 1.14 1.90

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