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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
NEURL1B ENST00000369800 39.26 31.06 33.32 0.90 1.04 0.89 1.75 1.36 1.71
PEAK1 ENST00000560626 39.26 21.25 28.43 0.90 1.40 0.78 1.75 0.81 1.30
SIKE1 ENST00000369528 39.27 37.21 36.35 0.90 0.77 0.85 1.75 1.66 1.87
TRAFD1 ENST00000257604 39.27 44.38 40.11 0.90 0.62 0.81 1.75 1.97 1.99
GIN1 ENST00000399004 39.28 46.48 41.09 0.90 0.73 0.76 1.75 2.02 2.06
FAM210B ENST00000371384 39.29 77.67 58.54 0.90 0.42 0.51 1.75 0.79 1.64
PLK3 ENST00000372201 39.29 38.69 37.29 0.90 0.70 0.84 1.75 1.67 2.01
STARD4 ENST00000296632 39.30 89.74 66.21 0.90 0.27 0.52 1.75 0.37 1.20
DIAPH3 ENST00000400324 39.30 37.95 36.82 0.90 0.78 0.82 1.75 1.70 1.94
DENND2C ENST00000393274 39.31 37.02 36.27 0.90 0.77 0.85 1.76 1.68 1.85
ADPRM ENST00000379774 39.31 61.01 49.09 0.90 0.54 0.72 1.76 1.41 1.82
COX17 ENST00000261070 39.32 79.93 60.06 0.89 0.37 0.47 1.76 0.61 1.61
DENND4C ENST00000602925 39.32 18.86 27.22 0.89 1.53 0.99 1.76 0.74 1.24
FSTL5 ENST00000306100 39.33 34.73 35.22 0.89 0.77 0.86 1.76 1.54 1.76
MEGF10 ENST00000274473 39.33 14.83 25.14 0.89 1.92 1.05 1.76 0.62 1.16
RPRM ENST00000325926 39.34 86.76 64.33 0.89 0.24 0.51 1.76 0.40 1.35
RNF169 ENST00000299563 39.34 27.68 31.71 0.89 1.27 0.89 1.76 1.19 1.58
MTHFD1L ENST00000367321 39.35 35.97 35.77 0.89 0.80 0.85 1.76 1.58 1.78
PSMA8 ENST00000308268 39.35 56.40 46.53 0.89 0.52 0.66 1.76 1.53 1.90
PDLIM3 ENST00000284770 39.36 62.34 49.82 0.89 0.53 0.65 1.76 1.33 1.90
MKS1 ENST00000393119 39.36 56.75 46.79 0.89 0.53 0.67 1.76 1.55 1.87
BCAS2 ENST00000369541 39.37 75.12 57.14 0.89 0.51 0.52 1.76 0.91 1.69
PSEN2 ENST00000366783 39.37 36.67 36.13 0.89 0.77 0.87 1.77 1.66 1.79
YIPF6 ENST00000462683 39.38 19.00 27.33 0.89 1.51 0.97 1.77 0.76 1.24
PMP2 ENST00000256103 39.38 72.55 55.65 0.89 0.47 0.53 1.77 1.04 1.72

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