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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
BAG6 ENST00000375964 20.28 4.79 10.09 1.53 3.28 2.24 1.01 0.32 0.43
IPPK ENST00000287996 20.28 16.41 16.16 1.53 1.80 1.71 1.02 0.69 0.66
KIAA1033 ENST00000332180 20.29 22.74 19.52 1.53 1.46 1.54 1.02 0.88 0.83
ZNF641 ENST00000544117 20.29 36.89 26.77 1.54 0.76 0.97 1.02 1.70 1.27
PTBP1 ENST00000356948 20.30 4.34 9.84 1.53 3.27 2.30 1.02 0.32 0.40
THRAP3 ENST00000354618 20.30 3.71 9.45 1.53 3.33 2.30 1.02 0.30 0.40
REEP2 ENST00000254901 20.31 28.33 22.50 1.53 1.16 1.16 1.02 1.22 0.97
PELI3 ENST00000320740 20.31 36.23 26.38 1.53 0.82 1.01 1.02 1.61 1.25
SLC39A8 ENST00000394833 20.32 23.06 19.71 1.53 1.46 1.53 1.03 0.91 0.85
SUCLA2 ENST00000378654 20.32 32.07 24.20 1.53 0.91 1.11 1.03 1.47 1.05
MFSD6 ENST00000392328 20.33 43.43 30.06 1.53 0.61 0.81 1.03 1.95 1.46
NR5A2 ENST00000367362 20.33 22.47 19.38 1.53 1.51 1.54 1.03 0.83 0.85
TARS2 ENST00000369064 20.34 45.75 31.27 1.53 0.75 0.86 1.03 2.02 1.55
PCOLCE2 ENST00000295992 20.35 67.34 42.09 1.53 0.56 0.71 1.03 1.20 1.99
ABCA1 ENST00000374736 20.35 23.07 19.75 1.52 1.46 1.52 1.03 0.91 0.85
F9 ENST00000218099 20.36 4.08 9.70 1.52 3.24 2.26 1.03 0.32 0.40
PIK3C2B ENST00000367187 20.36 10.86 13.21 1.52 2.11 2.09 1.03 0.50 0.53
CTTNBP2NL ENST00000271277 20.37 32.24 24.35 1.52 0.86 1.09 1.03 1.46 1.07
FER ENST00000281092 20.37 16.50 16.25 1.52 1.78 1.70 1.03 0.69 0.65
TOB2 ENST00000327492 20.38 20.53 18.39 1.52 1.43 1.66 1.03 0.78 0.81
TSHZ3 ENST00000240587 20.38 11.16 13.37 1.52 2.10 2.05 1.03 0.54 0.55
TCF12 ENST00000438423 20.39 17.64 16.84 1.53 1.58 1.70 1.03 0.73 0.70
ANKFY1 ENST00000570535 20.39 12.11 13.94 1.52 2.06 2.06 1.03 0.57 0.59
GABRG1 ENST00000295452 20.40 43.16 29.96 1.52 0.62 0.85 1.03 1.90 1.46
PAQR9 ENST00000340634 20.40 42.51 29.63 1.53 0.59 0.85 1.03 1.87 1.40

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