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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
ERCC6 ENST00000355832 57.60 42.04 48.68 0.57 0.59 0.68 1.53 1.84 1.85
STAMBPL1 ENST00000371926 57.60 65.20 62.22 0.57 0.51 0.48 1.53 1.24 1.43
SPACA4 ENST00000321762 57.61 93.88 79.06 0.57 0.25 0.39 1.53 0.26 0.53
RANGRF ENST00000226105 57.61 77.36 69.71 0.57 0.42 0.44 1.53 0.76 0.94
STOX1 ENST00000298596 57.62 62.82 60.81 0.57 0.51 0.43 1.53 1.29 1.60
RIBC1 ENST00000375327 57.62 11.15 32.57 0.57 2.10 0.87 1.53 0.54 1.63
SGSM3 ENST00000248929 57.63 49.53 52.91 0.57 0.66 0.61 1.53 2.03 1.87
METTL10 ENST00000368836 57.63 69.35 64.91 0.57 0.56 0.51 1.53 1.14 1.33
IL17A ENST00000340057 57.64 63.25 61.06 0.57 0.47 0.43 1.52 1.31 1.55
ARR3 ENST00000307959 57.64 30.01 42.05 0.57 1.09 0.70 1.51 1.43 1.99
VGLL2 ENST00000326274 57.65 29.69 41.86 0.57 1.11 0.68 1.52 1.39 2.01
CLPTM1L ENST00000320895 57.65 32.75 43.57 0.57 0.84 0.62 1.52 1.44 2.01
OTOP2 ENST00000331427 57.66 75.82 68.75 0.57 0.43 0.46 1.52 0.89 1.06
RGS14 ENST00000408923 57.66 27.01 40.54 0.57 1.23 0.80 1.52 1.12 2.04
IRX1 ENST00000302006 57.67 62.08 60.34 0.57 0.56 0.46 1.53 1.36 1.58
LOXL4 ENST00000260702 57.67 60.50 59.33 0.57 0.52 0.51 1.53 1.41 1.69
CMC1 ENST00000466830 57.68 70.41 65.61 0.57 0.52 0.51 1.53 1.08 1.29
SH2D4B ENST00000339284 57.68 45.62 50.73 0.57 0.73 0.66 1.53 2.00 1.84
ABCC12 ENST00000311303 57.69 70.38 65.59 0.57 0.52 0.51 1.53 1.09 1.29
RPL39L ENST00000296277 57.69 98.73 81.72 0.57 0.16 0.35 1.54 0.15 0.47
TMEM97 ENST00000226230 57.70 78.00 70.09 0.57 0.42 0.46 1.54 0.77 0.91
CRAMP1L ENST00000397412 57.70 19.77 36.99 0.57 1.42 0.78 1.54 0.74 1.94
CCDC170 ENST00000239374 57.71 72.46 66.81 0.57 0.48 0.53 1.54 1.03 1.20
AP4S1 ENST00000216366 57.71 82.40 72.78 0.57 0.34 0.43 1.54 0.52 0.81
SYNC ENST00000409190 57.72 46.16 51.01 0.57 0.73 0.66 1.55 2.04 1.87

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