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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
RNF13 ENST00000344229 34.74 48.43 39.94 0.95 0.63 0.81 1.80 2.02 2.01
CDKL1 ENST00000395834 34.75 61.07 46.56 0.95 0.54 0.66 1.80 1.39 1.90
PAQR3 ENST00000512733 34.75 51.41 41.32 0.94 0.63 0.73 1.80 1.89 2.02
PTPRZ1 ENST00000393386 34.76 11.54 21.24 0.94 2.10 1.40 1.80 0.57 0.90
PTPN14 ENST00000366956 34.76 16.64 23.77 0.92 1.72 1.13 1.80 0.71 1.02
MXI1 ENST00000332674 34.77 41.46 36.25 0.92 0.62 0.85 1.80 1.81 1.84
UEVLD ENST00000396197 34.77 44.55 37.92 0.92 0.65 0.85 1.81 1.97 2.02
CEP57 ENST00000325542 34.78 23.96 27.48 0.92 1.38 0.97 1.81 0.95 1.27
CTBP2 ENST00000309035 34.78 27.56 29.30 0.92 1.25 0.82 1.82 1.17 1.34
C12orf29 ENST00000356891 34.79 71.94 52.69 0.92 0.51 0.59 1.82 1.06 1.89
SEMA6A ENST00000343348 34.79 5.41 18.03 0.92 3.06 1.70 1.82 0.33 0.78
SCG3 ENST00000220478 34.80 35.01 33.06 0.92 0.75 0.85 1.83 1.57 1.66
ETHE1 ENST00000292147 34.80 76.55 55.31 0.92 0.42 0.49 1.83 0.83 1.73
CYTH4 ENST00000248901 34.81 32.84 32.03 0.92 0.84 0.90 1.83 1.44 1.60
PTPRR ENST00000283228 34.81 34.69 32.93 0.94 0.80 0.86 1.83 1.55 1.66
ZKSCAN5 ENST00000394170 34.82 21.38 26.26 0.94 1.44 1.01 1.83 0.80 1.26
LOXL3 ENST00000264094 34.82 46.37 38.92 0.94 0.73 0.80 1.83 2.04 2.06
MRPL1 ENST00000315567 34.83 55.84 43.70 0.94 0.52 0.61 1.83 1.58 2.01
GOLT1A ENST00000308302 34.83 52.56 41.92 0.94 0.67 0.68 1.83 1.82 2.01
PEX5 ENST00000434354 34.84 28.94 30.08 0.94 1.15 0.81 1.83 1.31 1.46
WDR92 ENST00000295121 34.84 34.73 32.96 0.94 0.77 0.86 1.83 1.55 1.67
MYO1F ENST00000338257 34.85 25.96 28.55 0.94 1.20 0.78 1.84 1.10 1.34
DSCR3 ENST00000309117 34.85 57.30 44.64 0.94 0.54 0.62 1.83 1.49 2.06
PDP2 ENST00000311765 34.86 55.92 43.74 0.94 0.49 0.61 1.83 1.56 2.02
OAT ENST00000368845 34.86 51.74 41.53 0.94 0.61 0.75 1.83 1.88 2.02

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