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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
NIT2 ENST00000394140 46.88 87.31 69.19 0.56 0.22 0.44 1.82 0.41 0.99
FANCG ENST00000378643 46.88 58.21 51.70 0.56 0.54 0.62 1.81 1.44 1.94
ACKR4 ENST00000249887 46.89 87.08 69.06 0.56 0.22 0.44 1.80 0.40 1.03
AKAP7 ENST00000431975 46.89 68.53 57.69 0.56 0.53 0.49 1.81 1.19 1.67
LRRC28 ENST00000301981 46.90 73.04 60.47 0.56 0.52 0.44 1.81 1.03 1.58
RPAP1 ENST00000304330 46.90 41.36 42.38 0.56 0.62 0.68 1.81 1.81 2.02
C8orf46 ENST00000305454 46.91 44.56 44.20 0.56 0.65 0.62 1.81 1.97 2.04
GSX1 ENST00000302945 46.91 62.10 54.00 0.56 0.54 0.59 1.81 1.36 1.77
HYAL3 ENST00000336307 46.92 71.51 59.51 0.56 0.53 0.49 1.81 1.07 1.70
LURAP1 ENST00000371980 46.92 64.43 55.34 0.56 0.48 0.49 1.81 1.22 1.73
ANO5 ENST00000324559 46.93 51.41 48.03 0.56 0.63 0.67 1.82 1.89 1.88
BLVRA ENST00000402924 46.93 50.75 47.64 0.56 0.63 0.65 1.82 1.94 1.88
MRPS14 ENST00000476371 46.94 85.59 68.26 0.57 0.27 0.52 1.82 0.44 1.08
ZXDC ENST00000389709 46.94 53.35 49.05 0.57 0.66 0.72 1.82 1.70 1.83
SRI ENST00000265729 46.95 78.70 64.10 0.57 0.40 0.52 1.82 0.73 1.37
KIF9 ENST00000335044 46.96 65.00 55.66 0.57 0.49 0.53 1.82 1.24 1.73
CCDC84 ENST00000334418 46.96 65.90 56.17 0.57 0.54 0.49 1.82 1.22 1.77
TTC8 ENST00000380656 46.97 38.91 41.14 0.57 0.70 0.75 1.82 1.65 2.02
AQP11 ENST00000313578 46.97 72.45 60.14 0.57 0.48 0.48 1.82 1.03 1.61
RTN4R ENST00000043402 46.98 12.50 27.89 0.57 2.07 0.85 1.82 0.59 1.29
PPP1R3A ENST00000284601 46.98 53.99 49.36 0.57 0.65 0.71 1.82 1.70 1.84
DDX47 ENST00000358007 46.99 53.98 49.41 0.57 0.65 0.70 1.81 1.70 1.83
COG1 ENST00000299886 46.99 32.02 37.74 0.57 0.92 0.84 1.81 1.48 2.01
SNAPC3 ENST00000380821 47.00 53.61 49.21 0.57 0.62 0.72 1.81 1.71 1.84
ARL9 ENST00000360096 47.00 46.07 45.21 0.56 0.76 0.70 1.81 2.03 2.00

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