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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
TSEN34 ENST00000396383 60.82 30.63 44.22 0.59 1.06 0.62 1.34 1.38 2.04
CBLN3 ENST00000267406 60.83 70.60 67.53 0.59 0.51 0.51 1.34 1.09 1.13
UTP18 ENST00000225298 60.83 33.49 45.86 0.59 0.84 0.68 1.35 1.53 1.97
SLCO4C1 ENST00000310954 60.84 41.57 50.24 0.59 0.63 0.65 1.36 1.80 1.90
GFER ENST00000248114 60.84 82.99 74.82 0.59 0.32 0.39 1.36 0.49 0.65
HEBP2 ENST00000607197 60.85 80.76 73.58 0.59 0.37 0.40 1.36 0.57 0.74
RBP5 ENST00000266560 60.85 81.92 74.25 0.59 0.35 0.39 1.36 0.51 0.69
AK7 ENST00000267584 60.86 45.10 52.21 0.59 0.68 0.61 1.36 1.97 1.89
F12 ENST00000253496 60.86 41.72 50.34 0.59 0.61 0.66 1.36 1.80 1.92
NOD1 ENST00000222823 60.87 63.67 63.43 0.59 0.49 0.49 1.36 1.23 1.38
GALE ENST00000374497 60.87 75.62 70.55 0.59 0.44 0.43 1.36 0.91 0.90
ARHGDIG ENST00000219409 60.88 16.87 37.11 0.59 1.66 0.81 1.36 0.71 1.95
MSGN1 ENST00000281047 60.89 80.02 73.19 0.59 0.37 0.43 1.36 0.60 0.79
SFXN1 ENST00000321442 60.89 42.08 50.49 0.59 0.61 0.67 1.36 1.85 1.87
CD109 ENST00000287097 60.90 65.34 64.40 0.59 0.52 0.51 1.36 1.25 1.34
SIRT4 ENST00000202967 60.90 87.61 77.45 0.59 0.23 0.35 1.36 0.37 0.58
APOH ENST00000205948 60.91 82.28 74.50 0.59 0.34 0.40 1.36 0.52 0.68
UQCRB ENST00000518406 60.91 61.07 61.71 0.58 0.54 0.46 1.36 1.39 1.46
ATXN7L1 ENST00000419735 60.92 7.29 32.31 0.58 2.58 0.90 1.36 0.37 1.61
MTERFD1 ENST00000287025 60.92 66.91 65.47 0.58 0.53 0.52 1.36 1.25 1.29
NLRC4 ENST00000404025 60.93 50.12 55.11 0.57 0.67 0.51 1.36 1.99 1.73
HK3 ENST00000292432 60.93 69.23 66.80 0.57 0.56 0.53 1.35 1.13 1.20
SLC36A2 ENST00000335244 60.94 70.03 67.25 0.57 0.53 0.52 1.35 1.14 1.16
RBM43 ENST00000331426 60.94 53.08 56.85 0.57 0.66 0.52 1.35 1.77 1.70
XRCC1 ENST00000262887 60.95 40.14 49.47 0.57 0.62 0.68 1.35 1.72 1.83

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