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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
CACNA1C ENST00000347598 2.98 1.23 0.64 3.90 4.00 4.65 0.30 0.27 0.19
DYNLL2 ENST00000579991 2.98 33.53 16.08 3.90 0.85 1.70 0.30 1.53 0.66
H2AFV ENST00000308153 2.99 48.17 23.68 3.90 0.63 1.16 0.30 1.97 1.01
TCEB1 ENST00000518127 2.99 34.77 16.75 3.90 0.77 1.70 0.30 1.55 0.70
CAMK2G ENST00000322680 3.00 8.79 3.32 3.89 2.47 3.90 0.30 0.48 0.24
PROX1 ENST00000366958 3.00 7.16 2.60 3.89 2.58 4.00 0.30 0.37 0.23
JAZF1 ENST00000283928 3.01 19.00 8.36 3.89 1.51 2.53 0.30 0.76 0.37
MAF1 ENST00000322428 3.01 15.52 6.65 3.89 1.87 3.01 0.30 0.67 0.32
EBF1 ENST00000313708 3.02 9.32 3.58 3.88 2.48 3.85 0.30 0.48 0.24
GRIN2A ENST00000396573 3.02 5.14 1.90 3.88 3.21 4.17 0.30 0.33 0.24
TRIM39 ENST00000376656 3.03 10.53 4.08 3.90 2.18 3.74 0.30 0.50 0.23
WNK1 ENST00000315939 3.03 2.02 0.87 3.89 3.73 4.51 0.30 0.28 0.20
ATP5B ENST00000262030 3.04 8.30 3.09 3.89 2.53 3.93 0.30 0.45 0.24
GRHL2 ENST00000251808 3.04 8.40 3.16 3.89 2.53 3.91 0.30 0.46 0.24
PRPF19 ENST00000227524 3.05 1.33 0.69 3.89 3.96 4.61 0.30 0.27 0.20
RNF145 ENST00000518802 3.05 13.03 5.30 3.88 2.07 3.56 0.30 0.59 0.25
KMT2B ENST00000222270 3.06 0.21 0.42 3.88 4.13 4.77 0.30 0.28 0.17
CPSF4 ENST00000292476 3.06 28.23 13.27 3.88 1.19 2.09 0.30 1.22 0.54
C9orf41 ENST00000376834 3.07 36.42 17.64 3.88 0.82 1.64 0.30 1.64 0.77
SCN1A ENST00000303395 3.07 0.18 0.41 3.87 4.13 4.77 0.30 0.28 0.17
JUNB ENST00000302754 3.08 23.31 10.81 3.87 1.43 2.20 0.30 0.93 0.43
FBXL15 ENST00000224862 3.08 52.60 25.99 3.87 0.68 0.99 0.30 1.82 1.25
GMEB1 ENST00000294409 3.09 11.39 4.55 3.87 2.10 3.70 0.30 0.56 0.25
HNRNPF ENST00000443950 3.09 11.33 4.51 3.88 2.11 3.70 0.30 0.56 0.25
YEATS4 ENST00000247843 3.10 59.47 29.45 3.88 0.51 0.85 0.30 1.41 1.36

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