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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
WDR24 ENST00000293883 23.89 35.42 27.81 1.37 0.77 0.90 1.11 1.55 1.27
HRAS ENST00000451590 23.90 49.49 34.87 1.37 0.65 0.90 1.11 2.03 1.75
FRMPD4 ENST00000380682 23.90 0.75 9.86 1.37 4.12 2.30 1.11 0.27 0.41
GTF2IRD1 ENST00000455841 23.91 14.19 16.90 1.37 2.06 1.68 1.11 0.60 0.71
SRSF12 ENST00000452027 23.91 39.85 30.08 1.37 0.65 0.81 1.11 1.69 1.46
PSIP1 ENST00000380733 23.92 7.35 13.24 1.37 2.56 2.09 1.10 0.37 0.53
YARS ENST00000373477 23.92 33.46 26.85 1.37 0.84 0.97 1.10 1.52 1.27
CPNE9 ENST00000383832 23.93 38.66 29.46 1.37 0.70 0.85 1.10 1.66 1.37
SBF2 ENST00000256190 23.93 22.42 21.27 1.37 1.51 1.39 1.10 0.82 0.90
POU4F2 ENST00000281321 23.94 51.97 36.05 1.35 0.61 0.87 1.10 1.85 1.78
SCMH1 ENST00000402904 23.95 37.29 28.75 1.34 0.76 0.80 1.10 1.66 1.33
PIGC ENST00000367728 23.95 56.16 38.35 1.34 0.52 0.85 1.10 1.55 2.04
OSBPL1A ENST00000319481 23.96 27.20 23.68 1.34 1.25 1.16 1.10 1.14 1.01
FJX1 ENST00000317811 23.96 13.97 16.82 1.34 2.06 1.70 1.10 0.60 0.70
SEMA3F ENST00000002829 23.97 7.06 13.06 1.34 2.57 2.09 1.11 0.37 0.52
FAM134C ENST00000309428 23.97 26.00 23.09 1.34 1.20 1.20 1.11 1.10 1.00
RFX2 ENST00000303657 23.98 6.81 12.95 1.34 2.63 2.09 1.10 0.37 0.53
CENPI ENST00000372927 23.98 1.32 10.21 1.35 3.96 2.21 1.10 0.27 0.42
FBXO9 ENST00000244426 23.99 33.36 26.82 1.35 0.85 0.97 1.10 1.51 1.28
CAMK4 ENST00000282356 23.99 23.59 21.92 1.35 1.39 1.18 1.10 0.93 0.96
AFF3 ENST00000356421 24.00 6.90 13.03 1.35 2.62 2.09 1.10 0.37 0.52
HSPA13 ENST00000285667 24.00 36.03 28.20 1.35 0.80 0.81 1.10 1.58 1.28
P2RY10 ENST00000171757 24.01 57.07 38.86 1.35 0.56 0.80 1.10 1.51 2.05
PLN ENST00000357525 24.01 80.34 51.26 1.35 0.37 0.63 1.10 0.58 1.92
NRP1 ENST00000265371 24.02 10.68 15.12 1.35 2.14 1.86 1.10 0.51 0.64

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