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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
VSIG10 ENST00000359236 57.08 47.74 51.55 0.56 0.59 0.62 1.57 1.99 1.93
TUT1 ENST00000308436 57.08 44.57 49.76 0.56 0.65 0.65 1.57 1.97 1.86
FAM57A ENST00000308278 57.09 37.62 46.07 0.56 0.78 0.68 1.58 1.71 1.97
CHST8 ENST00000262622 57.09 61.00 59.26 0.56 0.54 0.51 1.58 1.41 1.68
PADI3 ENST00000375460 57.10 50.14 53.01 0.56 0.67 0.61 1.58 1.99 1.87
NOX4 ENST00000263317 57.10 61.49 59.60 0.56 0.54 0.49 1.57 1.40 1.68
C9orf91 ENST00000288502 57.11 64.18 61.30 0.56 0.49 0.44 1.57 1.20 1.48
C3orf14 ENST00000494481 57.11 89.17 76.20 0.56 0.27 0.37 1.57 0.35 0.62
BBS12 ENST00000542236 57.12 53.75 55.02 0.56 0.63 0.51 1.57 1.70 1.73
TCTE1 ENST00000371505 57.13 78.99 70.36 0.56 0.40 0.43 1.57 0.69 0.91
SCN11A ENST00000302328 57.13 42.43 48.66 0.56 0.59 0.67 1.57 1.89 1.85
TIMP4 ENST00000287814 57.14 63.73 61.04 0.56 0.49 0.43 1.57 1.22 1.55
DNHD1 ENST00000254579 57.14 43.49 49.23 0.56 0.61 0.72 1.56 1.96 1.85
C4orf27 ENST00000393381 57.15 62.71 60.40 0.56 0.51 0.44 1.56 1.31 1.58
SLC35E4 ENST00000343605 57.15 59.31 58.27 0.56 0.51 0.47 1.56 1.41 1.65
AGTR2 ENST00000371906 57.16 72.55 66.51 0.56 0.47 0.51 1.56 1.04 1.21
SPACA1 ENST00000237201 57.16 41.50 48.20 0.54 0.62 0.66 1.56 1.82 1.87
PCCB ENST00000469217 57.17 48.14 51.81 0.54 0.63 0.62 1.56 1.97 1.92
XRCC2 ENST00000359321 57.17 74.45 67.66 0.54 0.53 0.51 1.56 1.00 1.13
CCNJL ENST00000393977 57.18 64.27 61.40 0.54 0.49 0.44 1.56 1.20 1.48
CXCR2 ENST00000318507 57.18 74.38 67.63 0.56 0.53 0.51 1.56 1.00 1.13
PGLYRP3 ENST00000290722 57.19 67.81 63.77 0.56 0.52 0.49 1.56 1.18 1.38
UGT1A6 ENST00000305139 57.19 59.08 58.24 0.56 0.49 0.47 1.56 1.44 1.65
CMBL ENST00000296658 57.20 61.26 59.52 0.56 0.53 0.49 1.57 1.40 1.70
OR10A2 ENST00000307322 57.20 84.27 73.53 0.56 0.28 0.40 1.57 0.44 0.74

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