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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
DNAH12 ENST00000311202 56.82 61.51 59.41 0.58 0.54 0.49 1.58 1.40 1.71
PTGR1 ENST00000407693 56.83 71.03 65.48 0.58 0.49 0.52 1.58 1.07 1.29
PROKR2 ENST00000546004 56.83 81.25 71.56 0.58 0.34 0.44 1.58 0.54 0.83
CHMP4C ENST00000297265 56.84 76.00 68.42 0.58 0.44 0.47 1.57 0.86 1.06
NPTX2 ENST00000265634 56.84 39.21 46.74 0.58 0.70 0.66 1.58 1.63 1.87
IL1B ENST00000263341 56.85 34.17 43.89 0.58 0.84 0.62 1.58 1.55 2.02
MRPS17 ENST00000285298 56.85 86.68 74.70 0.58 0.24 0.40 1.58 0.40 0.67
ACMSD ENST00000356140 56.86 61.27 59.28 0.58 0.53 0.51 1.59 1.39 1.68
PLG ENST00000308192 56.86 21.56 37.45 0.58 1.44 0.86 1.58 0.81 2.01
ROS1 ENST00000368508 56.87 60.26 58.65 0.58 0.53 0.52 1.58 1.38 1.65
GPR137B ENST00000366592 56.87 73.75 67.05 0.58 0.52 0.52 1.58 1.03 1.16
TRDMT1 ENST00000377799 56.88 65.81 62.12 0.58 0.54 0.48 1.58 1.22 1.44
CSRNP1 ENST00000273153 56.88 27.15 40.29 0.58 1.24 0.80 1.58 1.14 1.99
DFFB ENST00000378209 56.89 58.81 57.87 0.58 0.54 0.48 1.58 1.41 1.65
DUPD1 ENST00000338487 56.89 92.12 77.72 0.58 0.24 0.38 1.58 0.32 0.55
OR4D5 ENST00000307033 56.90 91.53 77.41 0.58 0.23 0.35 1.58 0.32 0.58
CLCA2 ENST00000370565 56.90 70.25 65.03 0.58 0.52 0.51 1.58 1.12 1.31
CYP24A1 ENST00000216862 56.91 79.49 70.54 0.58 0.38 0.43 1.58 0.66 0.91
EIF4EBP1 ENST00000338825 56.91 79.32 70.43 0.58 0.38 0.43 1.58 0.67 0.91
CTC1 ENST00000315684 56.92 33.09 43.37 0.58 0.84 0.63 1.58 1.49 2.01
INPP5E ENST00000371712 56.92 34.30 44.01 0.58 0.85 0.62 1.58 1.56 2.04
RASD1 ENST00000225688 56.93 66.82 62.85 0.58 0.54 0.51 1.58 1.23 1.40
SLBP ENST00000489418 56.93 40.94 47.77 0.58 0.61 0.65 1.57 1.78 1.88
C12orf56 ENST00000333722 56.94 83.10 72.73 0.58 0.29 0.43 1.57 0.49 0.81
IDNK ENST00000376419 56.94 35.64 44.94 0.57 0.78 0.68 1.57 1.58 2.03

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