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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
PCK2 ENST00000216780 51.91 75.93 65.48 0.61 0.43 0.52 1.81 0.86 1.29
NOL12 ENST00000359114 51.92 63.17 57.49 0.61 0.47 0.52 1.81 1.31 1.65
TCTN1 ENST00000397659 51.92 65.27 58.69 0.61 0.51 0.51 1.82 1.24 1.64
DHX57 ENST00000295373 51.93 35.14 41.76 0.61 0.76 0.72 1.82 1.58 2.01
APOA5 ENST00000542499 51.93 80.95 68.43 0.61 0.35 0.47 1.82 0.57 1.06
XCR1 ENST00000309285 51.94 57.01 53.94 0.61 0.56 0.61 1.82 1.52 1.77
NUP88 ENST00000573584 51.94 34.41 41.38 0.61 0.84 0.73 1.82 1.56 2.03
RRAD ENST00000299759 51.95 41.08 45.16 0.61 0.59 0.70 1.82 1.80 2.00
PANX3 ENST00000284288 51.95 63.66 57.81 0.61 0.49 0.51 1.82 1.23 1.67
ISCA2 ENST00000556816 51.96 94.18 76.10 0.61 0.25 0.38 1.82 0.25 0.62
NIPSNAP3A ENST00000374767 51.97 86.57 71.83 0.61 0.24 0.44 1.82 0.41 0.82
KRT1 ENST00000252244 51.97 19.61 33.97 0.61 1.43 0.90 1.82 0.74 1.73
AFF1 ENST00000395146 51.98 16.01 32.21 0.61 1.85 0.91 1.82 0.68 1.60
GJA9 ENST00000357771 51.98 80.62 68.28 0.61 0.37 0.52 1.82 0.57 1.07
IL4 ENST00000231449 51.99 79.10 67.33 0.61 0.39 0.52 1.82 0.69 1.15
PML ENST00000268058 51.99 20.71 34.57 0.59 1.47 0.90 1.82 0.80 1.77
SLC9C1 ENST00000305815 52.00 35.67 42.06 0.59 0.78 0.71 1.82 1.57 1.99
TRIM36 ENST00000282369 52.00 34.01 41.27 0.59 0.82 0.75 1.83 1.55 2.01
VTI1A ENST00000393077 52.01 44.50 46.99 0.61 0.63 0.70 1.83 1.97 1.87
ZIC4 ENST00000525172 52.01 47.18 48.45 0.61 0.66 0.67 1.83 2.00 1.87
MSH6 ENST00000234420 52.02 25.80 37.18 0.61 1.21 0.81 1.83 1.05 1.97
CKAP4 ENST00000378026 52.02 25.87 37.24 0.61 1.21 0.81 1.83 1.08 1.99
TIMELESS ENST00000553532 52.03 54.63 52.67 0.61 0.58 0.59 1.83 1.66 1.90
TIPIN ENST00000261881 52.03 59.03 55.11 0.61 0.51 0.51 1.83 1.43 1.73
TBC1D30 ENST00000539867 52.04 15.69 32.05 0.59 1.87 0.90 1.83 0.68 1.60

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