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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
RP11-1070N10.3 ENST00000554161 94.12 99.89 98.99 0.10 0.17 0.11 0.13 0.11 0.04
AL136531.1 ENST00000537552 94.12 99.90 98.68 0.10 0.17 0.10 0.13 0.11 0.05
AC074091.13 ENST00000379677 94.13 78.82 89.42 0.10 0.42 0.18 0.13 0.71 0.24
AC009892.10 ENST00000456337 94.13 96.79 97.94 0.10 0.23 0.09 0.13 0.19 0.04
C4orf48 ENST00000409248 94.14 74.11 87.29 0.10 0.53 0.28 0.13 1.03 0.31
RP11-863K10.7 ENST00000330539 94.14 99.90 99.00 0.10 0.17 0.11 0.13 0.10 0.04
LRRC53 ENST00000294635 94.15 76.29 88.36 0.10 0.43 0.22 0.13 0.86 0.30
SYNGR3 ENST00000248121 94.15 40.68 69.17 0.10 0.63 0.44 0.13 1.77 1.00
DEFB4B ENST00000318157 94.16 95.72 97.55 0.10 0.23 0.08 0.13 0.20 0.07
NKX2-8 ENST00000258829 94.16 74.19 87.12 0.10 0.53 0.28 0.13 1.03 0.30
SPRN ENST00000541506 94.17 93.32 96.51 0.10 0.28 0.07 0.13 0.29 0.07
SOCS1 ENST00000332029 94.17 60.75 80.76 0.10 0.56 0.39 0.13 1.40 0.52
C19orf81 ENST00000425202 94.18 83.13 91.53 0.10 0.29 0.15 0.13 0.49 0.18
DEFB105B ENST00000335510 94.18 93.56 96.66 0.10 0.28 0.08 0.13 0.28 0.08
AC117834.1 ENST00000391681 94.19 72.83 86.67 0.10 0.49 0.30 0.13 1.04 0.33
CCL4L1 ENST00000444414 94.19 93.10 94.23 0.10 0.28 0.10 0.13 0.30 0.12
C18orf63 ENST00000579455 94.20 37.54 67.73 0.10 0.80 0.52 0.13 1.67 1.12
NKX6-3 ENST00000524115 94.20 83.48 91.35 0.10 0.27 0.15 0.13 0.46 0.18
AP000322.53 ENST00000450895 94.21 83.07 91.49 0.10 0.30 0.15 0.13 0.49 0.18
FAM215A ENST00000588043 94.22 99.97 98.09 0.10 0.18 0.09 0.13 0.09 0.05
FHAD1 ENST00000375995 94.22 75.87 88.22 0.10 0.43 0.23 0.13 0.88 0.30
MTRNR2L4 ENST00000399974 94.23 99.97 97.70 0.10 0.18 0.09 0.13 0.09 0.06
METRN ENST00000568223 94.23 76.02 88.29 0.10 0.43 0.22 0.13 0.86 0.30
USP17L17 ENST00000511568 94.24 99.98 99.06 0.10 0.18 0.11 0.13 0.09 0.04
MTRNR2L1 ENST00000540040 94.24 99.99 98.52 0.10 0.18 0.10 0.12 0.09 0.05

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