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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
STAU2 ENST00000524300 17.70 13.47 13.18 1.47 2.05 2.10 0.89 0.60 0.52
PLD5 ENST00000536534 17.70 26.36 20.09 1.47 1.18 1.49 0.89 1.08 0.86
AAMP ENST00000248450 17.71 19.56 16.45 1.47 1.43 1.72 0.89 0.74 0.69
CDKAL1 ENST00000274695 17.71 26.58 20.21 1.47 1.19 1.48 0.89 1.11 0.88
TNFRSF1A ENST00000162749 17.72 7.78 10.28 1.47 2.54 2.20 0.89 0.43 0.42
SWAP70 ENST00000318950 17.72 23.09 18.37 1.47 1.46 1.64 0.89 0.91 0.80
RPL27 ENST00000589913 17.73 23.11 18.34 1.47 1.47 1.66 0.89 0.91 0.80
ROR1 ENST00000371079 17.73 7.42 10.12 1.48 2.54 2.24 0.89 0.39 0.42
UGP2 ENST00000337130 17.74 60.89 37.58 1.48 0.56 0.84 0.89 1.41 2.01
PTK7 ENST00000481273 17.74 10.69 11.83 1.49 2.14 2.21 0.89 0.51 0.46
VPS52 ENST00000445902 17.75 24.53 19.12 1.49 1.30 1.53 0.90 1.03 0.85
ZMAT4 ENST00000297737 17.75 39.70 26.90 1.49 0.66 0.97 0.90 1.66 1.27
DVL3 ENST00000313143 17.76 20.27 16.84 1.49 1.44 1.70 0.90 0.75 0.70
LSM4 ENST00000593829 17.76 54.79 34.50 1.49 0.56 0.90 0.90 1.63 1.77
CREM ENST00000345491 17.77 23.02 18.35 1.49 1.44 1.66 0.90 0.91 0.80
SCUBE3 ENST00000274938 17.77 9.42 11.26 1.49 2.48 2.16 0.90 0.49 0.45
ITK ENST00000422843 17.78 37.49 25.74 1.49 0.78 1.04 0.89 1.67 1.22
EOMES ENST00000295743 17.78 12.26 12.55 1.49 2.06 2.21 0.89 0.58 0.51
RAPH1 ENST00000319170 17.79 7.45 10.16 1.49 2.54 2.25 0.89 0.39 0.42
KMO ENST00000366559 17.79 34.52 24.19 1.49 0.80 1.11 0.89 1.56 1.05
SIDT2 ENST00000324225 17.80 34.68 24.26 1.49 0.80 1.10 0.89 1.54 1.05
PSME2 ENST00000216802 17.80 36.37 25.16 1.51 0.82 1.05 0.89 1.63 1.17
PKM ENST00000319622 17.81 22.18 17.91 1.51 1.53 1.68 0.89 0.81 0.77
GPR139 ENST00000570682 17.81 47.75 31.03 1.51 0.59 0.82 0.89 1.99 1.51
CLIP1 ENST00000540338 17.82 14.54 13.86 1.52 2.04 2.10 0.89 0.61 0.59

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