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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
C1orf204 ENST00000368102 90.78 91.83 94.28 0.16 0.23 0.10 0.22 0.32 0.12
ATP6V1G1 ENST00000374050 90.79 69.74 83.86 0.16 0.53 0.35 0.22 1.13 0.42
AC022498.1 ENST00000392468 90.79 98.13 97.40 0.16 0.20 0.08 0.22 0.16 0.07
SMCO2 ENST00000416383 90.80 78.73 88.14 0.16 0.42 0.23 0.22 0.73 0.30
C5orf47 ENST00000340147 90.80 93.45 95.47 0.16 0.28 0.08 0.21 0.28 0.11
DUX4L4 ENST00000538692 90.81 98.14 96.80 0.16 0.20 0.08 0.21 0.16 0.07
FAM133A ENST00000538690 90.81 53.45 75.25 0.16 0.65 0.37 0.21 1.72 0.67
RP11-553A10.1 ENST00000383686 90.82 94.70 94.96 0.16 0.23 0.09 0.21 0.24 0.10
AL049840.1 ENST00000429169 90.82 98.15 97.39 0.16 0.20 0.08 0.21 0.16 0.07
RP11-1C1.5 ENST00000506021 90.83 84.93 91.05 0.16 0.27 0.15 0.21 0.44 0.20
RP11-661C8.3 ENST00000511936 90.83 87.80 91.81 0.16 0.24 0.14 0.21 0.37 0.18
LRRC3C ENST00000377924 90.84 73.86 85.50 0.16 0.53 0.33 0.21 1.03 0.35
LACTBL1 ENST00000426928 90.84 61.41 79.60 0.16 0.54 0.38 0.21 1.40 0.52
ZNF487 ENST00000437590 90.85 90.35 92.90 0.16 0.25 0.14 0.21 0.38 0.15
AL359195.1 ENST00000356374 90.85 98.16 97.41 0.16 0.20 0.08 0.21 0.16 0.07
AC005008.2 ENST00000431501 90.86 91.76 94.29 0.16 0.24 0.10 0.21 0.32 0.12
AC131971.1 ENST00000332881 90.86 98.17 97.42 0.16 0.20 0.08 0.21 0.16 0.07
SMIM13 ENST00000416247 90.87 82.06 89.79 0.16 0.34 0.18 0.20 0.51 0.23
C19orf77 ENST00000215531 90.87 77.95 87.78 0.16 0.42 0.24 0.20 0.79 0.32
C17orf96 ENST00000325814 90.88 71.41 84.62 0.16 0.53 0.34 0.20 1.05 0.40
AC008394.1 ENST00000445770 90.88 94.49 95.18 0.16 0.23 0.09 0.20 0.24 0.10
ANKRD33B ENST00000296657 90.89 28.28 60.27 0.16 1.19 0.47 0.20 1.22 1.60
HSPB6 ENST00000592984 90.89 73.31 84.91 0.16 0.56 0.34 0.20 1.02 0.40
LRRC9 ENST00000445360 90.90 65.24 81.21 0.16 0.51 0.38 0.20 1.24 0.49
RP11-171N4.2 ENST00000511399 90.90 87.51 92.03 0.16 0.23 0.14 0.20 0.38 0.16

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