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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
PEAR1 ENST00000338302 63.28 48.64 55.64 0.59 0.63 0.53 1.25 2.00 1.73
PNLIPRP1 ENST00000528052 63.28 70.70 69.06 0.59 0.49 0.44 1.25 1.09 1.02
NPFFR2 ENST00000308744 63.29 63.24 64.61 0.59 0.47 0.51 1.25 1.31 1.32
GPR83 ENST00000243673 63.29 64.52 65.46 0.59 0.48 0.52 1.25 1.22 1.29
PCDHA2 ENST00000526136 63.30 78.92 73.89 0.59 0.40 0.40 1.25 0.70 0.70
SERINC4 ENST00000319327 63.30 79.72 74.40 0.59 0.37 0.40 1.25 0.64 0.70
CYB5RL ENST00000419823 63.31 64.39 65.33 0.59 0.48 0.53 1.25 1.22 1.32
OR1A1 ENST00000304094 63.31 86.78 78.30 0.59 0.24 0.38 1.25 0.40 0.54
CLPS ENST00000259938 63.32 81.64 75.41 0.59 0.33 0.37 1.25 0.52 0.65
PIFO ENST00000369738 63.32 80.06 74.61 0.59 0.37 0.40 1.25 0.60 0.68
AGTRAP ENST00000314340 63.33 50.03 56.51 0.59 0.66 0.52 1.25 2.01 1.70
PEPD ENST00000244137 63.33 67.02 66.90 0.59 0.53 0.53 1.25 1.24 1.20
SMPD2 ENST00000258052 63.34 82.84 76.13 0.59 0.32 0.37 1.25 0.50 0.62
CLCNKB ENST00000375679 63.34 67.88 67.41 0.59 0.52 0.52 1.25 1.17 1.14
COL6A6 ENST00000358511 63.35 55.07 59.50 0.59 0.58 0.49 1.24 1.63 1.70
PRSS16 ENST00000230582 63.35 43.05 52.52 0.59 0.61 0.61 1.24 1.89 1.90
ATOH8 ENST00000306279 63.36 17.69 38.82 0.59 1.54 0.82 1.24 0.73 2.04
RCN1 ENST00000054950 63.36 57.74 61.19 0.59 0.57 0.43 1.24 1.46 1.49
PMPCA ENST00000371717 63.37 59.98 62.54 0.59 0.53 0.48 1.24 1.37 1.39
DRAXIN ENST00000294485 63.37 81.14 75.18 0.59 0.35 0.38 1.24 0.55 0.67
HMHA1 ENST00000539243 63.38 14.52 37.23 0.59 2.04 0.81 1.23 0.61 1.99
TM4SF5 ENST00000270560 63.39 59.97 62.54 0.59 0.53 0.48 1.23 1.37 1.40
WBP2 ENST00000591399 63.39 30.64 45.69 0.59 1.06 0.68 1.23 1.38 2.00
S100A3 ENST00000368713 63.40 89.77 79.90 0.59 0.27 0.37 1.24 0.37 0.52
LPP ENST00000312675 63.40 28.22 44.27 0.59 1.19 0.61 1.24 1.22 2.05

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