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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
ZMYM6 ENST00000357182 29.32 36.57 31.13 1.10 0.78 0.84 1.56 1.63 1.55
VAV3 ENST00000370056 29.32 38.45 32.07 1.10 0.75 0.90 1.56 1.70 1.60
BCL7A ENST00000538010 29.33 38.03 31.87 1.10 0.77 0.91 1.57 1.71 1.58
LARP6 ENST00000299213 29.33 26.34 25.99 1.10 1.19 0.99 1.57 1.08 1.25
PTH ENST00000282091 29.34 86.77 58.13 1.10 0.24 0.48 1.57 0.40 1.66
VASH1 ENST00000167106 29.34 31.86 28.72 1.10 0.94 0.80 1.57 1.48 1.34
MIER2 ENST00000264819 29.35 15.70 20.65 1.10 1.87 1.47 1.57 0.68 0.88
BRINP2 ENST00000361539 29.35 6.50 15.74 1.10 2.63 1.77 1.56 0.37 0.66
FAM122B ENST00000343004 29.36 22.89 24.14 1.10 1.47 1.11 1.56 0.90 1.05
TNNC2 ENST00000372555 29.36 59.23 42.56 1.10 0.49 0.68 1.56 1.44 2.01
PHLDB1 ENST00000361417 29.37 17.62 21.61 1.10 1.57 1.27 1.56 0.73 0.93
SMPD3 ENST00000219334 29.37 21.45 23.51 1.10 1.43 1.18 1.55 0.80 1.01
NIPAL4 ENST00000311946 29.38 48.66 37.31 1.10 0.63 0.84 1.55 1.99 2.02
SCP2 ENST00000371514 29.38 40.47 33.08 1.10 0.62 0.87 1.55 1.76 1.66
MLXIP ENST00000319080 29.39 11.91 18.63 1.10 2.10 1.59 1.55 0.58 0.81
CDC16 ENST00000360383 29.39 17.31 21.49 1.10 1.61 1.30 1.55 0.75 0.91
FLRT1 ENST00000246841 29.40 31.48 28.59 1.10 0.96 0.80 1.55 1.43 1.35
JAK2 ENST00000381652 29.40 15.60 20.63 1.10 1.87 1.48 1.55 0.68 0.88
TMOD2 ENST00000249700 29.41 34.81 30.31 1.10 0.76 0.84 1.55 1.55 1.44
FAM120AOS ENST00000375412 29.41 39.02 32.42 1.10 0.70 0.91 1.55 1.64 1.61
PDIA3 ENST00000300289 29.42 8.67 16.88 1.10 2.48 1.68 1.55 0.47 0.70
RPA2 ENST00000373912 29.43 26.03 25.87 1.09 1.20 1.01 1.55 1.10 1.23
MORC1 ENST00000232603 29.43 26.35 26.05 1.08 1.19 0.99 1.55 1.08 1.25
ATXN7L2 ENST00000369870 29.44 14.03 19.79 1.08 2.06 1.49 1.55 0.59 0.85
BICD2 ENST00000356884 29.44 13.11 19.28 1.08 2.06 1.52 1.55 0.59 0.85

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