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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
INSL5 ENST00000304526 95.56 88.65 94.86 0.11 0.24 0.09 0.11 0.35 0.11
GOLGA8A ENST00000360553 95.56 89.14 95.09 0.11 0.27 0.09 0.11 0.35 0.10
ATXN3L ENST00000380622 95.57 99.87 99.35 0.11 0.17 0.11 0.11 0.11 0.04
FCRL6 ENST00000368106 95.57 89.32 95.19 0.11 0.27 0.08 0.11 0.37 0.10
IL3RA ENST00000331035 95.58 91.28 96.15 0.11 0.23 0.07 0.11 0.34 0.10
EID2B ENST00000326282 95.58 99.25 98.94 0.11 0.15 0.10 0.11 0.13 0.04
TCEAL2 ENST00000372780 95.59 89.63 95.35 0.11 0.27 0.08 0.11 0.36 0.10
KIAA1551 ENST00000312561 95.59 18.76 57.05 0.11 1.52 0.51 0.11 0.74 1.71
MYEOV2 ENST00000307266 95.60 79.65 90.67 0.11 0.37 0.15 0.11 0.65 0.20
ZNF747 ENST00000252799 95.60 77.84 89.82 0.11 0.42 0.18 0.11 0.79 0.23
SLC22A10 ENST00000332793 95.61 79.29 90.51 0.11 0.38 0.14 0.11 0.67 0.21
IQCF3 ENST00000456080 95.61 96.50 98.36 0.11 0.22 0.10 0.11 0.19 0.05
AC016722.1 ENST00000409912 95.62 96.67 98.41 0.11 0.23 0.10 0.11 0.20 0.05
IFNA16 ENST00000380216 95.63 98.74 99.26 0.11 0.16 0.11 0.11 0.14 0.04
SAA1 ENST00000405158 95.63 84.17 92.65 0.11 0.27 0.14 0.11 0.44 0.15
CEACAM6 ENST00000199764 95.64 70.71 86.37 0.11 0.49 0.33 0.11 1.09 0.33
C1orf86 ENST00000378546 95.64 39.28 69.65 0.11 0.70 0.44 0.11 1.65 0.95
NUTM2A ENST00000381707 95.65 96.68 98.41 0.11 0.23 0.10 0.11 0.20 0.05
TMEM61 ENST00000371268 95.65 90.66 95.88 0.11 0.25 0.07 0.11 0.36 0.11
C16orf3 ENST00000408886 95.66 98.10 98.95 0.11 0.20 0.10 0.11 0.16 0.04
AC011484.1 ENST00000377652 95.66 98.47 98.73 0.11 0.21 0.10 0.11 0.14 0.05
HUS1B ENST00000380907 95.67 99.70 99.32 0.11 0.17 0.11 0.11 0.11 0.04
KIR2DL1 ENST00000336077 95.67 93.69 97.35 0.11 0.28 0.08 0.11 0.27 0.07
MXRA5 ENST00000217939 95.68 19.03 57.24 0.11 1.51 0.52 0.11 0.76 1.69
CEACAM7 ENST00000006724 95.68 79.45 90.64 0.11 0.38 0.15 0.12 0.67 0.20

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