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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
CELSR3 ENST00000164024 20.67 9.03 12.42 1.56 2.43 2.23 1.00 0.47 0.50
PPP2R5B ENST00000164133 14.47 12.35 11.06 1.56 2.06 2.20 0.73 0.59 0.45
PYGM ENST00000164139 35.18 48.23 40.02 0.91 0.63 0.82 1.85 1.99 1.99
BCL3 ENST00000164227 67.95 7.04 35.64 0.58 2.57 0.85 1.03 0.37 1.77
PIGB ENST00000164305 73.32 60.32 68.83 0.34 0.53 0.46 0.80 1.39 1.05
PDZD4 ENST00000164640 32.07 18.06 23.17 0.97 1.53 1.19 1.72 0.74 1.02
PRLH ENST00000165524 94.80 93.04 96.72 0.10 0.28 0.08 0.11 0.30 0.08
FSTL3 ENST00000166139 57.44 17.66 35.69 0.58 1.58 0.85 1.55 0.73 1.76
EPHA8 ENST00000166244 61.05 35.79 47.18 0.59 0.78 0.67 1.34 1.59 1.89
TRIP13 ENST00000166345 9.05 8.99 6.33 2.33 2.45 3.09 0.46 0.47 0.32
VASH1 ENST00000167106 29.34 31.86 28.72 1.10 0.94 0.80 1.57 1.48 1.34
KRT14 ENST00000167586 29.00 45.02 35.18 1.10 0.68 0.86 1.54 1.96 1.75
KRT20 ENST00000167588 72.80 70.29 74.47 0.32 0.52 0.40 0.79 1.10 0.69
SPP2 ENST00000168148 84.16 92.91 91.44 0.32 0.29 0.15 0.48 0.30 0.18
HSD17B10 ENST00000168216 0.58 19.28 7.28 4.38 1.47 2.80 0.19 0.76 0.34
FGF4 ENST00000168712 56.04 60.46 58.30 0.58 0.52 0.48 1.62 1.41 1.65
NMRK2 ENST00000168977 86.71 94.88 93.53 0.24 0.23 0.13 0.40 0.23 0.15
ST6GAL1 ENST00000169298 18.76 29.35 22.20 1.56 1.10 1.15 0.91 1.36 0.96
TIMM21 ENST00000169551 71.12 61.80 68.45 0.42 0.57 0.47 0.85 1.37 1.06
BPIFB2 ENST00000170150 71.73 67.12 72.03 0.35 0.54 0.43 0.81 1.22 0.81
REXO1 ENST00000170168 79.51 12.69 44.66 0.34 2.10 0.62 0.57 0.58 2.06
MKRN2 ENST00000170447 51.58 36.79 42.44 0.59 0.76 0.68 1.85 1.65 2.01
GPATCH1 ENST00000170564 47.86 34.62 39.59 0.52 0.80 0.80 1.80 1.54 2.04
KEAP1 ENST00000171111 8.05 32.36 18.16 2.58 0.87 1.66 0.43 1.46 0.79
P2RY10 ENST00000171757 24.01 57.07 38.86 1.35 0.56 0.80 1.10 1.51 2.05

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