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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
RPS6KA2 ENST00000503859 40.03 22.35 29.37 0.86 1.51 0.82 1.75 0.82 1.36
CETN1 ENST00000327228 40.04 79.77 60.37 0.86 0.37 0.46 1.75 0.64 1.58
TINAGL1 ENST00000271064 40.04 33.79 35.09 0.86 0.85 0.86 1.75 1.55 1.75
PMS1 ENST00000441310 40.05 53.76 45.62 0.86 0.63 0.68 1.75 1.71 1.98
TTLL1 ENST00000266254 40.05 41.65 39.23 0.86 0.62 0.78 1.75 1.80 2.04
ATP1B2 ENST00000250111 40.06 31.82 34.12 0.86 0.94 0.89 1.75 1.48 1.75
NUDT5 ENST00000491614 40.07 47.24 41.89 0.86 0.66 0.68 1.75 2.00 2.01
CDO1 ENST00000250535 40.07 50.76 43.77 0.86 0.63 0.61 1.75 1.95 2.01
LDB3 ENST00000429277 40.08 36.81 36.55 0.86 0.76 0.85 1.75 1.66 1.90
LYPD6B ENST00000409642 40.08 60.45 49.18 0.86 0.53 0.72 1.75 1.41 1.84
STX12 ENST00000373943 40.09 14.48 25.38 0.86 2.04 1.05 1.74 0.61 1.17
E2F6 ENST00000381525 40.09 30.90 33.66 0.86 1.08 0.90 1.74 1.36 1.73
HOXB9 ENST00000311177 40.10 40.83 38.73 0.86 0.61 0.82 1.74 1.78 2.02
VGLL4 ENST00000430365 40.10 51.83 44.50 0.86 0.61 0.61 1.75 1.87 2.04
EXOSC3 ENST00000327304 40.11 61.17 49.57 0.86 0.53 0.67 1.75 1.40 1.85
CSF3R ENST00000373103 40.11 41.42 39.12 0.86 0.62 0.77 1.75 1.80 2.06
GALNT11 ENST00000434507 40.12 34.13 35.32 0.86 0.84 0.87 1.75 1.54 1.76
WDR55 ENST00000358337 40.12 82.71 62.25 0.86 0.34 0.48 1.75 0.50 1.43
PTP4A3 ENST00000521578 40.13 60.33 49.13 0.86 0.53 0.72 1.75 1.40 1.83
SPINK6 ENST00000325630 40.13 96.64 70.72 0.86 0.23 0.43 1.75 0.20 0.87
C5orf15 ENST00000231512 40.14 60.06 48.97 0.86 0.53 0.71 1.75 1.37 1.84
DGAT2 ENST00000228027 40.14 68.20 53.60 0.86 0.52 0.63 1.75 1.21 1.81
NSMCE4A ENST00000369023 40.15 37.09 36.80 0.86 0.78 0.82 1.75 1.66 1.94
NDUFAF5 ENST00000378106 40.15 64.36 51.37 0.86 0.49 0.63 1.75 1.21 1.90
DAPK3 ENST00000545797 40.16 36.43 36.39 0.86 0.82 0.84 1.74 1.64 1.87

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