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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
GRAMD4 ENST00000406902 21.96 3.37 10.22 1.52 3.43 2.21 1.03 0.29 0.42
PHF3 ENST00000262043 21.96 11.36 14.42 1.52 2.10 2.00 1.03 0.56 0.59
ALCAM ENST00000306107 21.97 18.08 17.95 1.52 1.53 1.71 1.03 0.74 0.78
AREL1 ENST00000356357 21.97 30.27 24.13 1.51 1.09 1.11 1.03 1.39 1.06
WDR13 ENST00000218056 21.98 18.66 18.26 1.51 1.51 1.66 1.03 0.75 0.79
TRPV4 ENST00000418703 21.98 57.96 38.28 1.51 0.56 0.85 1.03 1.46 2.04
TOMM34 ENST00000372813 21.99 36.58 27.42 1.52 0.78 0.96 1.03 1.63 1.27
ATXN1 ENST00000244769 21.99 12.75 15.14 1.52 2.09 1.85 1.03 0.59 0.64
CNN1 ENST00000252456 22.00 35.57 26.95 1.52 0.77 1.00 1.03 1.58 1.27
DGKH ENST00000337343 22.00 17.74 17.77 1.51 1.53 1.66 1.04 0.72 0.78
CAMK2N1 ENST00000375078 22.01 85.24 53.02 1.51 0.25 0.61 1.04 0.45 1.87
C10orf2 ENST00000311916 22.01 32.90 25.54 1.51 0.82 1.05 1.04 1.44 1.19
RANBP3 ENST00000340578 22.02 2.80 9.97 1.49 3.52 2.26 1.04 0.28 0.42
COL11A2 ENST00000374708 22.02 13.42 15.54 1.49 2.05 1.80 1.04 0.60 0.67
RTCB ENST00000216038 22.03 30.45 24.27 1.49 1.09 1.10 1.04 1.38 1.06
GRIN3A ENST00000361820 22.03 17.41 17.59 1.49 1.61 1.63 1.04 0.73 0.77
PC ENST00000393960 22.04 22.13 20.16 1.49 1.52 1.48 1.04 0.83 0.87
SLC16A12 ENST00000371790 22.04 23.23 20.78 1.49 1.43 1.47 1.04 0.92 0.88
PI15 ENST00000260113 22.05 40.84 29.62 1.49 0.61 0.85 1.04 1.78 1.39
PLXNB1 ENST00000358536 22.05 18.00 17.95 1.49 1.52 1.71 1.04 0.74 0.77
PARD6A ENST00000219255 22.06 66.03 42.31 1.49 0.56 0.70 1.04 1.21 2.01
RWDD4 ENST00000326397 22.06 42.40 30.46 1.49 0.59 0.80 1.03 1.90 1.46
KLHL32 ENST00000369261 22.07 29.09 23.69 1.48 1.14 1.16 1.03 1.32 1.01
KIF21B ENST00000422435 22.08 19.88 18.97 1.48 1.42 1.54 1.03 0.73 0.83
CRIM1 ENST00000280527 22.08 7.89 12.51 1.48 2.54 2.21 1.03 0.44 0.51

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