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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
KRTAP9-9 ENST00000394008 87.04 93.51 93.01 0.23 0.28 0.14 0.39 0.28 0.15
ZSCAN32 ENST00000304926 87.04 81.16 87.28 0.23 0.35 0.28 0.39 0.55 0.31
EPPIN ENST00000555685 87.05 64.12 78.81 0.23 0.49 0.39 0.38 1.20 0.52
EPPIN-WFDC6 ENST00000504988 87.05 64.14 78.84 0.23 0.49 0.39 0.38 1.21 0.52
A3GALT2 ENST00000442999 87.06 81.31 87.37 0.23 0.33 0.28 0.38 0.54 0.31
ZNF124 ENST00000340684 87.06 86.69 89.95 0.23 0.24 0.18 0.38 0.40 0.23
PRR22 ENST00000419421 87.07 84.73 89.02 0.23 0.27 0.19 0.38 0.42 0.26
FPR3 ENST00000339223 87.07 98.36 95.58 0.23 0.21 0.08 0.38 0.14 0.11
CSNK2A3 ENST00000528848 87.08 85.81 89.58 0.23 0.28 0.18 0.38 0.44 0.23
ZNF563 ENST00000293725 87.08 32.93 60.49 0.23 0.82 0.44 0.38 1.46 1.58
AP5Z1 ENST00000348624 87.09 79.15 86.33 0.23 0.39 0.33 0.38 0.69 0.33
PGLYRP1 ENST00000008938 87.09 89.74 91.33 0.23 0.27 0.15 0.38 0.37 0.18
KRTAP10-5 ENST00000400372 87.10 71.96 82.89 0.23 0.51 0.32 0.38 1.06 0.40
EVPLL ENST00000399134 87.10 74.20 83.94 0.23 0.53 0.35 0.38 1.02 0.43
GOLGA6A ENST00000290438 87.11 80.61 87.06 0.23 0.37 0.28 0.38 0.57 0.30
VHLL ENST00000339922 87.11 97.58 95.09 0.23 0.22 0.09 0.38 0.20 0.10
C8orf82 ENST00000524821 87.12 91.85 92.14 0.23 0.23 0.14 0.38 0.32 0.16
TUBB8 ENST00000309812 87.12 79.47 86.50 0.23 0.38 0.30 0.38 0.66 0.33
ZNF429 ENST00000358491 87.13 93.43 93.03 0.23 0.28 0.14 0.38 0.28 0.15
IL33 ENST00000381434 87.13 88.23 90.75 0.23 0.23 0.15 0.38 0.37 0.20
RPSAP58 ENST00000496398 87.14 85.22 89.28 0.23 0.25 0.19 0.38 0.45 0.25
MZB1 ENST00000302125 87.14 75.76 84.83 0.23 0.43 0.34 0.38 0.88 0.40
ZNF670 ENST00000366503 87.15 90.37 91.60 0.23 0.25 0.14 0.38 0.37 0.18
PSORS1C2 ENST00000259845 87.15 87.82 90.56 0.23 0.24 0.15 0.38 0.38 0.21
FAM180B ENST00000356737 87.16 69.21 81.55 0.23 0.56 0.35 0.38 1.12 0.48

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