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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
ATG7 ENST00000354449 38.87 48.92 42.13 0.91 0.65 0.71 1.74 2.04 2.00
RAD54B ENST00000336148 38.88 48.21 41.77 0.91 0.63 0.72 1.74 1.99 2.01
DARS2 ENST00000361951 38.88 50.07 42.80 0.91 0.67 0.70 1.75 1.99 2.02
COG2 ENST00000366669 38.89 31.09 33.14 0.91 1.02 0.87 1.75 1.36 1.68
CDNF ENST00000465530 38.89 88.76 65.31 0.91 0.25 0.53 1.75 0.36 1.32
URM1 ENST00000452446 38.90 71.57 54.82 0.91 0.53 0.53 1.75 1.07 1.74
CCDC126 ENST00000307471 38.90 66.88 52.14 0.91 0.53 0.61 1.75 1.24 1.91
CSRP1 ENST00000367306 38.91 63.39 50.16 0.91 0.48 0.63 1.75 1.29 1.90
LAMA2 ENST00000421865 38.91 38.58 36.96 0.91 0.72 0.78 1.76 1.67 1.95
SERPINH1 ENST00000524558 38.92 38.09 36.64 0.91 0.77 0.84 1.75 1.70 1.92
ASAH2B ENST00000374006 38.92 87.48 64.54 0.91 0.23 0.51 1.75 0.39 1.33
NUP214 ENST00000359428 38.93 15.15 25.11 0.91 1.90 1.05 1.75 0.66 1.16
MSH4 ENST00000263187 38.93 51.15 43.39 0.91 0.66 0.63 1.75 1.91 2.00
KDSR ENST00000406396 38.94 29.53 32.44 0.90 1.10 0.91 1.75 1.39 1.61
MSMO1 ENST00000261507 38.94 38.47 36.92 0.90 0.73 0.80 1.75 1.69 1.94
GCG ENST00000418842 38.95 52.81 44.37 0.90 0.65 0.62 1.75 1.80 2.03
VAV2 ENST00000371850 38.95 26.55 30.95 0.90 1.19 0.81 1.75 1.12 1.51
SCRN3 ENST00000272732 38.96 62.98 49.95 0.90 0.49 0.61 1.75 1.31 1.90
TSSC1 ENST00000382125 38.96 25.33 30.33 0.90 1.28 0.84 1.75 1.03 1.45
ARMC5 ENST00000268314 38.97 25.91 30.69 0.90 1.21 0.80 1.75 1.09 1.48
NDUFB9 ENST00000276689 38.98 57.39 46.90 0.90 0.54 0.70 1.75 1.49 1.87
PCSK7 ENST00000320934 38.98 26.49 30.93 0.90 1.18 0.80 1.75 1.10 1.51
GPRC5B ENST00000300571 38.99 37.13 36.19 0.90 0.80 0.87 1.75 1.66 1.83
HPS1 ENST00000325103 38.99 36.27 35.75 0.90 0.82 0.85 1.76 1.61 1.78
TMEM215 ENST00000342743 39.00 82.14 61.24 0.90 0.34 0.43 1.76 0.51 1.48

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