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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
PTPN13 ENST00000436978 49.69 31.88 39.14 0.54 0.94 0.77 1.84 1.48 2.07
MAP7D2 ENST00000379643 49.71 22.32 34.29 0.54 1.52 0.87 1.84 0.82 1.76
FYTTD1 ENST00000241502 49.71 27.13 36.52 0.54 1.23 0.85 1.84 1.14 1.90
PKD2L1 ENST00000318222 49.72 68.58 59.40 0.54 0.53 0.49 1.84 1.19 1.71
SNTG1 ENST00000522124 49.72 19.82 32.94 0.54 1.42 0.86 1.84 0.74 1.67
EBAG9 ENST00000337573 49.73 37.98 42.08 0.54 0.77 0.71 1.84 1.71 1.99
RPL13A ENST00000391857 49.73 21.92 34.01 0.54 1.46 0.89 1.84 0.81 1.72
ARV1 ENST00000310256 50.70 68.52 60.04 0.61 0.53 0.48 1.84 1.20 1.61
SLC25A38 ENST00000273158 50.72 60.02 54.94 0.59 0.53 0.51 1.84 1.37 1.74
LZTR1 ENST00000215739 50.72 97.50 77.25 0.59 0.22 0.35 1.84 0.19 0.58
KREMEN1 ENST00000327813 50.73 33.95 40.54 0.59 0.84 0.80 1.84 1.55 2.04
CLCN1 ENST00000343257 50.73 55.27 52.23 0.59 0.57 0.59 1.84 1.62 1.90
IGLON5 ENST00000270642 50.74 30.11 38.67 0.59 1.08 0.82 1.84 1.41 2.02
JPH1 ENST00000342232 50.96 18.73 32.99 0.62 1.52 0.85 1.84 0.74 1.67
AKR1D1 ENST00000242375 50.96 61.55 55.93 0.62 0.54 0.49 1.84 1.41 1.76
JAKMIP3 ENST00000298622 51.22 14.01 30.86 0.59 2.06 0.77 1.84 0.59 1.49
ERMP1 ENST00000339450 51.22 47.64 48.30 0.59 0.62 0.67 1.84 1.97 1.89
TIMM23 ENST00000260867 51.23 60.87 55.74 0.59 0.56 0.53 1.84 1.41 1.74
DDX56 ENST00000258772 51.23 45.19 46.96 0.59 0.70 0.70 1.84 1.98 1.86
GLDC ENST00000321612 51.24 59.21 54.81 0.59 0.49 0.53 1.84 1.44 1.74
EMP3 ENST00000270221 51.24 80.42 67.69 0.59 0.37 0.52 1.84 0.59 1.12
FGD5 ENST00000285046 51.25 3.62 25.53 0.59 3.36 1.05 1.84 0.30 1.19
PRPH ENST00000257860 51.32 76.32 65.32 0.59 0.43 0.53 1.84 0.86 1.32
TMPO ENST00000266732 51.32 54.65 52.23 0.59 0.58 0.59 1.84 1.65 1.90
A2M ENST00000318602 51.33 27.59 37.68 0.59 1.25 0.82 1.84 1.17 2.01

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