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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
FSCN3 ENST00000265825 51.57 58.23 54.45 0.59 0.54 0.57 1.85 1.43 1.75
MKRN2 ENST00000170447 51.58 36.79 42.44 0.59 0.76 0.68 1.85 1.65 2.01
NENF ENST00000366988 51.62 77.47 66.22 0.58 0.42 0.52 1.85 0.76 1.20
ZNF397 ENST00000330501 51.62 44.32 46.67 0.58 0.61 0.66 1.85 1.95 1.87
ATP9B ENST00000426216 51.63 34.89 41.48 0.58 0.76 0.73 1.85 1.55 2.02
PGAM1 ENST00000334828 51.63 84.65 70.47 0.58 0.27 0.43 1.85 0.42 0.91
MXD1 ENST00000264444 51.64 39.55 44.00 0.58 0.68 0.62 1.85 1.65 2.03
FOXC2 ENST00000320354 51.65 42.05 45.56 0.58 0.59 0.70 1.85 1.85 1.97
HIST1H2AG ENST00000359193 51.67 96.76 77.42 0.58 0.23 0.35 1.85 0.19 0.58
ZBTB8B ENST00000609129 34.94 47.64 39.64 0.94 0.61 0.80 1.85 1.97 2.05
HOXC4 ENST00000430889 34.95 42.11 36.68 0.94 0.61 0.84 1.85 1.86 1.93
HOXC4 ENST00000609810 34.95 42.15 36.74 0.92 0.61 0.82 1.85 1.87 1.94
ST7L ENST00000358039 34.96 47.24 39.43 0.92 0.66 0.77 1.85 2.00 2.04
KCNN4 ENST00000262888 34.96 54.44 43.06 0.92 0.61 0.66 1.85 1.67 2.01
HSPG2 ENST00000374695 34.97 18.71 24.89 0.92 1.52 1.02 1.85 0.74 1.11
TACR1 ENST00000305249 34.97 51.08 41.24 0.92 0.65 0.75 1.85 1.92 2.01
TSPAN18 ENST00000340160 34.98 38.33 34.82 0.92 0.75 0.90 1.85 1.71 1.76
UTP11L ENST00000373014 34.98 62.29 47.40 0.92 0.53 0.65 1.85 1.33 1.87
BRD2 ENST00000395289 35.09 6.80 18.93 0.94 2.64 1.54 1.85 0.37 0.83
SRPR ENST00000332118 35.11 12.45 21.91 0.92 2.06 1.18 1.85 0.59 0.96
WDR54 ENST00000348227 35.16 72.09 53.04 0.91 0.52 0.61 1.85 1.04 1.86
SEZ6L ENST00000248933 35.16 17.30 24.25 0.91 1.61 1.10 1.85 0.75 1.05
UNC13D ENST00000207549 35.17 41.27 36.34 0.91 0.61 0.85 1.85 1.82 1.87
PYGM ENST00000164139 35.18 48.23 40.02 0.91 0.63 0.82 1.85 1.99 1.99
VGLL3 ENST00000398399 35.19 41.17 36.29 0.92 0.59 0.85 1.85 1.82 1.86

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