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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
RP1-32I10.10 ENST00000406912 91.56 89.95 92.68 0.15 0.25 0.14 0.21 0.37 0.15
CTD-2616J11.4 ENST00000574814 91.56 90.36 93.95 0.15 0.25 0.09 0.20 0.37 0.11
DLEU7 ENST00000400393 91.57 83.39 90.77 0.15 0.27 0.15 0.20 0.47 0.20
AC092675.3 ENST00000409490 91.57 88.25 92.89 0.15 0.23 0.14 0.20 0.37 0.15
LINC00692 ENST00000451284 91.58 63.05 80.86 0.15 0.48 0.39 0.20 1.31 0.51
AC009365.3 ENST00000332558 91.58 86.90 92.13 0.15 0.22 0.14 0.20 0.41 0.16
STMND1 ENST00000536551 91.59 81.44 89.84 0.15 0.33 0.18 0.20 0.54 0.23
CLEC2A ENST00000455827 91.59 91.45 94.48 0.15 0.23 0.10 0.20 0.32 0.12
H2BFM ENST00000355016 91.60 84.36 91.02 0.15 0.29 0.15 0.20 0.44 0.20
C10orf85 ENST00000369071 91.60 98.49 97.24 0.15 0.21 0.08 0.20 0.15 0.06
PTPN20A ENST00000374339 91.61 93.59 94.67 0.15 0.28 0.09 0.20 0.28 0.11
RP11-738G5.2 ENST00000520800 91.61 91.74 94.63 0.15 0.24 0.09 0.20 0.32 0.11
C11orf91 ENST00000379011 91.62 89.32 93.45 0.15 0.27 0.11 0.20 0.37 0.15
NUPR1L ENST00000329309 91.62 96.33 96.12 0.15 0.22 0.07 0.20 0.19 0.10
AC018470.1 ENST00000595354 91.63 55.74 77.07 0.15 0.52 0.37 0.20 1.59 0.61
TDRD12 ENST00000421545 91.63 77.09 87.00 0.14 0.42 0.28 0.20 0.78 0.30
PATE4 ENST00000457514 91.64 91.68 93.87 0.14 0.24 0.09 0.20 0.32 0.12
AC127496.1 ENST00000321930 91.64 98.52 97.92 0.14 0.21 0.09 0.20 0.15 0.04
MGC10955 ENST00000401851 91.65 98.53 97.06 0.14 0.21 0.08 0.20 0.15 0.07
HMX1 ENST00000400677 91.65 40.56 68.32 0.14 0.63 0.49 0.20 1.76 1.07
FAM229A ENST00000432622 91.66 94.92 95.60 0.14 0.23 0.08 0.20 0.23 0.11
RP11-366L20.2 ENST00000356215 91.66 91.84 94.69 0.14 0.23 0.09 0.20 0.32 0.11
VSIG10L ENST00000335624 91.67 55.41 76.90 0.14 0.58 0.35 0.20 1.60 0.60
CCDC42B ENST00000335621 91.67 51.73 74.04 0.14 0.61 0.38 0.20 1.88 0.69
C2orf82 ENST00000409230 91.68 57.14 77.09 0.14 0.56 0.37 0.20 1.50 0.61

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