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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
GJB4 ENST00000339480 66.50 87.97 80.56 0.59 0.25 0.39 1.03 0.37 0.51
SPATA22 ENST00000573128 66.51 39.71 52.36 0.59 0.66 0.61 1.04 1.66 1.90
REEP5 ENST00000379638 66.52 69.49 70.26 0.59 0.54 0.43 1.04 1.12 0.91
TRIOBP ENST00000406386 66.52 37.37 51.02 0.59 0.76 0.66 1.04 1.66 1.87
TMEM70 ENST00000312184 66.53 58.95 64.02 0.59 0.52 0.52 1.04 1.42 1.39
GK2 ENST00000358842 66.53 75.64 73.86 0.59 0.44 0.42 1.04 0.91 0.71
AP000322.54 ENST00000410005 66.54 67.56 69.13 0.59 0.53 0.43 1.04 1.20 1.00
CCDC90B ENST00000529689 66.54 60.58 65.00 0.59 0.53 0.51 1.04 1.41 1.31
STK32B ENST00000282908 66.55 52.82 60.13 0.59 0.65 0.47 1.05 1.80 1.61
NR2F6 ENST00000291442 66.55 34.30 49.30 0.59 0.85 0.70 1.05 1.57 1.85
RASL12 ENST00000220062 66.56 66.86 68.73 0.59 0.53 0.46 1.05 1.24 1.05
PRSS36 ENST00000268281 66.56 60.77 65.11 0.59 0.56 0.51 1.04 1.39 1.31
MEGF11 ENST00000409699 66.57 61.79 65.77 0.59 0.57 0.51 1.04 1.37 1.26
C10orf54 ENST00000394957 66.57 22.92 43.12 0.61 1.47 0.65 1.04 0.90 2.00
OLFML1 ENST00000329293 66.58 69.35 70.20 0.61 0.56 0.43 1.04 1.14 0.91
SREK1IP1 ENST00000513458 66.58 36.83 50.78 0.61 0.76 0.66 1.04 1.66 1.84
OR11L1 ENST00000355784 66.59 57.15 62.85 0.61 0.56 0.51 1.04 1.50 1.40
MYO7B ENST00000428314 66.59 39.31 52.17 0.61 0.70 0.61 1.04 1.64 1.90
CCR2 ENST00000292301 66.60 53.16 60.36 0.61 0.66 0.46 1.04 1.76 1.58
MFAP2 ENST00000375535 66.60 67.91 69.41 0.61 0.52 0.43 1.04 1.17 0.98
DCST1 ENST00000295542 66.61 62.37 66.16 0.61 0.53 0.52 1.04 1.33 1.20
SEC61B ENST00000223641 66.61 78.34 75.42 0.61 0.43 0.37 1.05 0.74 0.66
EREG ENST00000244869 66.62 81.71 77.34 0.62 0.33 0.35 1.05 0.52 0.58
SLC27A1 ENST00000252595 66.62 63.30 66.68 0.62 0.47 0.53 1.05 1.31 1.20
RAB36 ENST00000263116 66.63 68.14 69.57 0.62 0.53 0.44 1.05 1.22 0.95

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