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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
THPO ENST00000204615 38.23 35.81 35.25 0.91 0.78 0.86 1.74 1.59 1.76
MON1A ENST00000296473 38.23 57.85 46.76 0.91 0.57 0.67 1.74 1.47 1.87
IRAK4 ENST00000448290 38.24 57.31 46.43 0.91 0.54 0.67 1.74 1.49 1.92
SLC25A13 ENST00000416240 38.24 62.99 49.53 0.91 0.48 0.67 1.74 1.31 1.85
METTL5 ENST00000260953 38.25 70.77 54.00 0.91 0.48 0.59 1.74 1.08 1.77
ARL13B ENST00000394222 38.25 53.79 44.56 0.91 0.63 0.62 1.74 1.70 2.04
PRR14 ENST00000542965 38.26 24.18 29.40 0.91 1.33 0.84 1.73 0.98 1.36
LGR6 ENST00000367278 38.26 32.17 33.37 0.92 0.86 0.87 1.73 1.46 1.72
ACTR8 ENST00000335754 38.27 55.86 45.76 0.92 0.51 0.68 1.73 1.57 1.97
HSD17B4 ENST00000504811 38.27 36.20 35.44 0.92 0.82 0.87 1.73 1.61 1.76
WDR17 ENST00000280190 38.28 45.89 40.35 0.92 0.75 0.80 1.73 2.03 2.01
SYCP3 ENST00000392927 38.28 50.50 42.69 0.91 0.63 0.68 1.73 1.94 2.02
SLC16A14 ENST00000295190 38.29 34.28 34.51 0.91 0.85 0.90 1.73 1.56 1.77
PHACTR4 ENST00000373836 38.29 36.35 35.49 0.91 0.82 0.87 1.73 1.63 1.77
NGFR ENST00000172229 38.30 27.72 31.23 0.91 1.27 0.86 1.73 1.18 1.56
CHCHD3 ENST00000262570 38.30 32.67 33.66 0.91 0.85 0.90 1.73 1.45 1.72
HS6ST1 ENST00000259241 38.31 17.40 26.01 0.91 1.59 0.99 1.73 0.73 1.25
ICA1 ENST00000402384 38.31 30.40 32.55 0.91 1.08 0.89 1.73 1.39 1.62
ZNF567 ENST00000585696 38.32 54.11 44.84 0.91 0.65 0.67 1.73 1.68 2.04
DAW1 ENST00000309931 38.32 41.68 38.29 0.91 0.62 0.85 1.73 1.80 2.04
DOCK5 ENST00000276440 38.33 20.56 27.59 0.91 1.44 0.96 1.73 0.76 1.25
GATAD2A ENST00000360315 38.33 6.39 20.48 0.91 2.66 1.49 1.73 0.37 0.89
KRTCAP2 ENST00000295682 38.34 76.80 57.51 0.91 0.42 0.52 1.73 0.81 1.66
SLC7A8 ENST00000316902 38.35 55.76 45.75 0.91 0.52 0.67 1.73 1.58 1.98
MANF ENST00000528157 38.35 79.15 58.87 0.91 0.39 0.49 1.73 0.69 1.65

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