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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
PADI2 ENST00000375486 55.53 45.02 49.19 0.61 0.68 0.72 1.66 1.97 1.84
NHLRC1 ENST00000340650 55.53 51.98 53.20 0.61 0.61 0.61 1.66 1.85 1.88
MRPL3 ENST00000264995 55.54 74.22 66.53 0.61 0.53 0.51 1.66 1.02 1.21
MCC ENST00000408903 55.54 44.31 48.84 0.61 0.61 0.70 1.66 1.95 1.85
GLIPR2 ENST00000377960 55.55 84.89 72.98 0.61 0.27 0.40 1.66 0.44 0.80
PCSK9 ENST00000302118 55.55 74.25 66.57 0.61 0.53 0.52 1.66 1.02 1.21
CERKL ENST00000339098 55.56 79.05 69.46 0.61 0.40 0.44 1.66 0.70 0.98
SMAGP ENST00000603798 55.57 71.87 65.17 0.61 0.51 0.52 1.66 1.07 1.31
NOTCH4 ENST00000375023 55.57 39.32 46.16 0.61 0.70 0.67 1.66 1.64 1.97
SLC25A40 ENST00000341119 55.58 57.91 56.55 0.61 0.57 0.52 1.66 1.46 1.70
COL16A1 ENST00000373672 55.58 33.21 42.70 0.61 0.82 0.68 1.66 1.50 2.02
RTTN ENST00000255674 55.59 38.21 45.60 0.61 0.77 0.68 1.65 1.70 1.98
OR6C75 ENST00000343399 55.59 80.52 70.35 0.61 0.37 0.43 1.65 0.59 0.90
GALR2 ENST00000329003 55.60 85.21 73.13 0.61 0.25 0.42 1.65 0.45 0.79
AC007431.1 ENST00000299415 55.60 43.43 48.39 0.61 0.61 0.67 1.65 1.95 1.88
FMO4 ENST00000367749 55.61 64.88 60.85 0.61 0.48 0.43 1.65 1.24 1.60
ALDH4A1 ENST00000375341 55.61 37.99 45.51 0.61 0.77 0.70 1.65 1.71 1.97
CABLES2 ENST00000279101 55.62 46.62 50.12 0.59 0.75 0.63 1.65 1.99 1.90
C20orf26 ENST00000245957 55.62 38.05 45.53 0.59 0.77 0.70 1.65 1.70 1.97
DDX59 ENST00000331314 55.63 47.60 50.66 0.59 0.61 0.66 1.65 2.00 1.85
RBP1 ENST00000232219 55.63 83.24 72.05 0.59 0.28 0.43 1.65 0.47 0.81
MYOC ENST00000037502 55.64 68.42 63.10 0.59 0.52 0.49 1.65 1.21 1.39
MOCS1 ENST00000373186 55.64 58.04 56.66 0.59 0.53 0.52 1.65 1.45 1.71
MOV10L1 ENST00000262794 55.65 41.46 47.30 0.59 0.62 0.66 1.65 1.82 1.87
PHKG1 ENST00000452681 55.65 69.20 63.63 0.59 0.56 0.49 1.65 1.13 1.39

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