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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
TMEM168 ENST00000312814 26.35 33.65 28.19 1.33 0.84 0.82 1.26 1.55 1.28
PNISR ENST00000369239 26.35 4.91 13.23 1.33 3.26 2.09 1.27 0.31 0.53
LETM1 ENST00000302787 26.36 39.64 31.19 1.33 0.68 0.85 1.27 1.65 1.55
C2CD2L ENST00000336702 26.36 12.31 17.18 1.33 2.06 1.64 1.27 0.59 0.73
TPCN1 ENST00000550785 26.37 19.99 21.30 1.33 1.44 1.39 1.27 0.73 0.91
MMP14 ENST00000311852 26.37 10.19 16.09 1.33 2.30 1.70 1.27 0.49 0.66
PTPRD ENST00000381196 26.38 1.02 11.40 1.33 4.06 2.19 1.28 0.28 0.45
RP11-176H8.1 ENST00000547378 26.38 71.02 47.46 1.34 0.49 0.63 1.27 1.07 1.89
CYFIP1 ENST00000313077 26.39 12.48 17.29 1.34 2.07 1.64 1.27 0.59 0.74
FBXO34 ENST00000313833 26.39 27.45 24.97 1.34 1.25 1.02 1.27 1.17 1.14
FSTL1 ENST00000295633 26.40 17.05 19.80 1.33 1.62 1.49 1.27 0.74 0.85
LMBRD2 ENST00000296603 26.40 22.91 22.79 1.33 1.47 1.19 1.27 0.90 0.98
P2RY12 ENST00000302632 26.41 74.94 49.61 1.33 0.53 0.67 1.28 0.94 1.84
CDKN1C ENST00000414822 26.41 27.09 24.78 1.33 1.23 1.04 1.28 1.12 1.10
AP1AR ENST00000274000 26.42 29.06 25.89 1.33 1.14 1.01 1.28 1.32 1.22
PCDHGC4 ENST00000306593 26.42 13.50 17.89 1.33 2.06 1.68 1.28 0.61 0.77
SH3BP5 ENST00000383791 26.43 31.66 27.19 1.33 0.92 0.99 1.28 1.45 1.25
RBM42 ENST00000262633 26.43 24.09 23.38 1.33 1.37 1.19 1.28 0.98 0.99
SSR3 ENST00000265044 26.44 27.19 24.85 1.33 1.24 1.02 1.29 1.14 1.10
NIPA1 ENST00000337435 26.44 49.42 36.04 1.33 0.65 0.87 1.29 2.01 1.78
FRMD3 ENST00000304195 26.45 21.60 22.12 1.33 1.44 1.16 1.29 0.81 0.97
ADPGK ENST00000311669 26.46 38.49 30.73 1.33 0.73 0.78 1.29 1.69 1.48
DSCAML1 ENST00000321322 26.46 3.66 12.62 1.33 3.35 2.20 1.29 0.31 0.52
RUFY2 ENST00000388768 26.47 26.04 24.30 1.33 1.20 1.09 1.29 1.10 1.06
MARCH3 ENST00000308660 26.47 41.49 32.18 1.33 0.62 0.91 1.29 1.82 1.60

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