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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
CD247 ENST00000362089 53.98 41.88 46.62 0.63 0.61 0.66 1.73 1.82 1.87
TRMT2B ENST00000372936 53.98 59.56 56.60 0.65 0.52 0.52 1.73 1.40 1.71
POLG ENST00000268124 53.99 29.03 39.85 0.65 1.15 0.77 1.74 1.31 2.02
SLC25A10 ENST00000571730 54.00 57.37 55.30 0.65 0.54 0.49 1.74 1.49 1.73
CYP7A1 ENST00000301645 54.00 43.37 47.45 0.65 0.59 0.63 1.74 1.95 1.88
SNX7 ENST00000306121 54.01 41.91 46.64 0.65 0.61 0.66 1.73 1.82 1.87
HSD17B3 ENST00000375263 54.01 58.44 55.90 0.65 0.54 0.49 1.73 1.39 1.75
AIMP1 ENST00000394701 54.02 67.62 61.52 0.65 0.53 0.46 1.73 1.19 1.48
IMP4 ENST00000259239 54.02 55.44 54.28 0.65 0.58 0.59 1.73 1.60 1.73
METTL18 ENST00000310392 54.03 75.16 66.28 0.65 0.51 0.52 1.73 0.91 1.21
WISP1 ENST00000250160 54.03 60.67 57.23 0.65 0.54 0.52 1.73 1.40 1.69
DNAJA4 ENST00000394855 54.04 41.99 46.70 0.65 0.59 0.66 1.73 1.83 1.86
C3orf67 ENST00000295966 54.04 50.60 51.45 0.65 0.63 0.63 1.74 1.95 1.91
APOBEC4 ENST00000308641 54.05 76.68 67.10 0.65 0.40 0.51 1.74 0.83 1.16
RIN3 ENST00000216487 54.05 47.86 49.93 0.65 0.59 0.61 1.74 1.98 1.89
RIC8A ENST00000325207 54.06 40.02 45.70 0.65 0.63 0.68 1.74 1.68 1.99
SYCE1 ENST00000343131 54.06 53.07 52.91 0.63 0.66 0.61 1.74 1.77 1.87
TRAPPC6B ENST00000330149 54.07 72.73 64.78 0.63 0.48 0.49 1.74 1.04 1.32
ACADVL ENST00000543245 54.07 59.59 56.64 0.63 0.52 0.52 1.73 1.41 1.72
RNASE4 ENST00000555835 54.08 93.68 77.03 0.63 0.28 0.37 1.73 0.27 0.61
NPHS1 ENST00000378910 54.08 36.22 43.54 0.63 0.82 0.62 1.73 1.61 2.01
ARL5A ENST00000295087 54.09 43.81 47.80 0.63 0.61 0.65 1.73 1.96 1.89
BRI3BP ENST00000341446 54.09 43.76 47.76 0.63 0.62 0.65 1.73 1.96 1.88
SLC36A4 ENST00000326402 54.10 83.49 71.26 0.63 0.27 0.44 1.73 0.46 0.87
ADAM12 ENST00000368679 54.10 29.99 40.31 0.63 1.09 0.80 1.73 1.41 2.00

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