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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
REL ENST00000295025 15.89 7.57 9.17 1.52 2.51 2.32 0.79 0.42 0.38
ZIC3 ENST00000287538 15.89 16.08 13.65 1.52 1.82 2.02 0.79 0.69 0.57
CTDSP2 ENST00000398073 15.90 34.42 23.23 1.52 0.82 1.19 0.79 1.56 1.01
NPLOC4 ENST00000331134 15.90 2.28 6.41 1.52 3.65 3.06 0.79 0.29 0.32
FADS3 ENST00000278829 15.91 32.12 22.15 1.52 0.89 1.15 0.79 1.46 0.96
ATF1 ENST00000262053 15.91 23.33 17.48 1.52 1.43 1.62 0.79 0.93 0.75
ZCCHC6 ENST00000375963 15.92 1.38 5.92 1.52 3.95 3.29 0.79 0.27 0.29
CXCR5 ENST00000292174 15.92 29.86 21.03 1.52 1.13 1.43 0.79 1.40 0.89
SEPT11 ENST00000264893 15.93 15.88 13.54 1.52 1.89 2.05 0.79 0.68 0.57
PANK1 ENST00000307534 15.93 32.10 22.17 1.52 0.90 1.15 0.79 1.46 0.96
POLR3A ENST00000372371 15.94 46.93 29.60 1.52 0.71 0.85 0.79 1.94 1.39
TBX3 ENST00000257566 15.94 11.60 11.45 1.52 2.10 2.21 0.79 0.57 0.45
CTSS ENST00000368985 15.95 26.43 19.18 1.52 1.16 1.53 0.79 1.09 0.85
G2E3 ENST00000206595 15.95 13.49 12.32 1.52 2.05 2.25 0.79 0.61 0.50
PAFAH1B2 ENST00000527958 15.96 16.21 13.74 1.52 1.80 2.06 0.79 0.70 0.58
FBXL7 ENST00000504595 15.97 26.94 19.46 1.52 1.23 1.53 0.79 1.12 0.84
TP53I11 ENST00000533940 15.97 42.29 27.27 1.52 0.61 0.97 0.79 1.89 1.25
ATF7IP ENST00000261168 15.98 5.22 7.97 1.53 3.16 2.59 0.79 0.32 0.36
HNRNPM ENST00000325495 15.98 0.92 5.68 1.53 4.10 3.34 0.79 0.29 0.27
ASUN ENST00000261191 15.99 13.84 12.47 1.53 2.05 2.23 0.79 0.60 0.50
SPEN ENST00000375759 15.99 0.24 5.45 1.53 4.13 3.44 0.79 0.28 0.26
TOX3 ENST00000219746 16.00 4.57 7.65 1.53 3.24 2.71 0.79 0.32 0.33
NEK6 ENST00000373600 16.00 32.77 22.59 1.53 0.84 1.18 0.79 1.44 0.96
GDI2 ENST00000380191 16.01 18.47 15.06 1.53 1.48 1.87 0.79 0.76 0.62
ABL2 ENST00000502732 16.01 29.52 20.90 1.53 1.10 1.44 0.79 1.39 0.87

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