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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
CHST2 ENST00000309575 37.62 43.51 38.89 0.92 0.59 0.80 1.76 1.97 2.06
ZBTB39 ENST00000300101 38.70 46.62 40.86 0.92 0.75 0.80 1.75 1.99 2.06
DEPDC1 ENST00000456315 38.74 42.87 39.18 0.92 0.62 0.78 1.75 1.92 2.06
CDON ENST00000392693 39.19 41.98 38.90 0.90 0.61 0.80 1.77 1.83 2.06
GIN1 ENST00000399004 39.28 46.48 41.09 0.90 0.73 0.76 1.75 2.02 2.06
MANEAL ENST00000373045 39.44 46.05 40.95 0.90 0.77 0.77 1.78 2.04 2.06
USP53 ENST00000450251 39.66 41.74 39.05 0.90 0.61 0.78 1.73 1.78 2.06
CYP19A1 ENST00000396402 39.77 52.43 44.67 0.89 0.65 0.62 1.74 1.83 2.06
RNF122 ENST00000256257 40.47 40.99 39.05 0.86 0.61 0.78 1.73 1.80 2.06
BTBD1 ENST00000261721 40.90 44.51 40.89 0.84 0.63 0.78 1.72 1.98 2.06
EIF4E3 ENST00000425534 42.41 43.38 41.10 0.76 0.61 0.76 1.75 1.95 2.06
CTNNAL1 ENST00000325551 42.78 42.99 41.10 0.78 0.62 0.76 1.77 1.89 2.06
FAM73A ENST00000370791 43.28 37.94 38.93 0.81 0.78 0.80 1.80 1.70 2.06
DNAJC16 ENST00000375847 43.73 41.97 41.06 0.76 0.61 0.75 1.79 1.83 2.06
TBC1D32 ENST00000398212 43.77 48.46 44.69 0.75 0.63 0.62 1.78 2.02 2.06
AP4B1 ENST00000369569 43.91 41.38 40.85 0.73 0.62 0.80 1.78 1.80 2.06
ZNF10 ENST00000248211 44.28 36.92 38.93 0.68 0.75 0.80 1.77 1.70 2.06
TRPV6 ENST00000359396 45.34 36.09 39.06 0.61 0.81 0.78 1.75 1.59 2.06
ACER2 ENST00000340967 45.92 35.72 39.20 0.58 0.78 0.78 1.78 1.58 2.06
TBC1D9B ENST00000356834 46.28 34.91 38.92 0.56 0.76 0.80 1.79 1.54 2.06
FRAS1 ENST00000264895 48.62 33.07 39.21 0.51 0.84 0.78 1.82 1.49 2.06
NOV ENST00000259526 49.55 42.69 44.69 0.54 0.61 0.62 1.82 1.91 2.06
BAIAP2L1 ENST00000005260 50.07 35.32 40.88 0.54 0.77 0.78 1.81 1.58 2.06
SLC7A6OS ENST00000263997 50.13 31.01 38.90 0.57 1.05 0.80 1.80 1.36 2.06
GBX1 ENST00000297537 50.61 34.79 40.89 0.59 0.77 0.77 1.81 1.55 2.06

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