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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
ARG1 ENST00000356962 34.61 51.11 41.08 0.97 0.66 0.76 1.79 1.92 2.04
TIE1 ENST00000372476 34.62 50.22 40.61 0.97 0.67 0.81 1.79 1.99 2.05
EMC8 ENST00000253457 34.62 21.27 26.11 0.97 1.42 0.97 1.80 0.81 1.26
ATP6V1E1 ENST00000253413 34.63 25.36 28.16 0.97 1.28 0.82 1.80 1.03 1.27
MFN1 ENST00000471841 34.63 42.27 36.57 0.97 0.61 0.85 1.80 1.89 1.91
RYR1 ENST00000359596 34.64 21.74 26.31 0.97 1.46 1.00 1.80 0.81 1.25
TULP1 ENST00000229771 34.64 31.49 31.27 0.97 0.96 0.86 1.79 1.43 1.55
L2HGDH ENST00000267436 34.65 41.37 36.12 0.97 0.62 0.89 1.78 1.80 1.80
IFT122 ENST00000296266 34.65 45.08 38.15 0.97 0.67 0.86 1.78 1.97 2.04
INTS4 ENST00000534064 34.66 37.32 34.27 0.96 0.76 0.87 1.78 1.66 1.75
TEX12 ENST00000280358 34.66 74.27 53.92 0.96 0.53 0.61 1.79 1.01 1.77
RAPSN ENST00000298854 34.67 39.11 35.07 0.95 0.70 0.86 1.79 1.63 1.75
TNRC6C ENST00000335749 34.67 2.04 16.17 0.95 3.72 1.71 1.80 0.29 0.66
FAM135B ENST00000395297 34.68 7.85 19.24 0.95 2.54 1.54 1.80 0.44 0.85
DHODH ENST00000219240 34.68 37.76 34.46 0.95 0.80 0.90 1.80 1.70 1.76
SART3 ENST00000228284 34.69 10.97 20.97 0.95 2.09 1.43 1.80 0.52 0.88
SALL4 ENST00000217086 34.69 1.39 15.87 0.95 3.94 1.77 1.80 0.27 0.66
SMARCAL1 ENST00000357276 34.70 31.51 31.33 0.95 0.96 0.87 1.80 1.43 1.55
IGBP1 ENST00000342206 34.70 8.07 19.40 0.95 2.53 1.54 1.80 0.44 0.85
SLC2A4 ENST00000317370 34.71 43.61 37.39 0.95 0.62 0.85 1.80 1.95 2.00
SRPRB ENST00000466490 34.71 43.17 37.19 0.95 0.62 0.81 1.80 1.91 1.97
SLC39A7 ENST00000374677 34.72 32.70 31.93 0.95 0.85 0.91 1.80 1.45 1.58
APBA2 ENST00000558402 34.72 17.31 24.06 0.95 1.61 1.10 1.80 0.75 1.06
EVI5L ENST00000538904 34.73 4.80 17.68 0.95 3.28 1.67 1.80 0.32 0.78
DMGDH ENST00000255189 34.73 64.99 48.73 0.95 0.49 0.68 1.80 1.24 1.85

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