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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
KIAA1279 ENST00000361983 16.27 25.06 18.67 1.48 1.33 1.58 0.80 1.03 0.81
TRAF4 ENST00000262395 16.28 15.66 13.60 1.48 1.87 2.01 0.80 0.69 0.57
MYBL1 ENST00000522677 16.29 0.65 5.71 1.48 4.12 3.33 0.80 0.28 0.28
USP8 ENST00000433963 16.29 1.50 6.15 1.48 3.90 3.20 0.80 0.26 0.30
PSTPIP2 ENST00000409746 16.30 28.87 20.73 1.48 1.15 1.46 0.81 1.30 0.88
CCNY ENST00000374704 16.30 19.29 15.63 1.48 1.46 1.75 0.81 0.76 0.67
KLF2 ENST00000248071 16.31 37.48 24.94 1.48 0.77 1.02 0.81 1.67 1.12
PHACTR2 ENST00000440869 16.31 31.36 21.94 1.48 0.97 1.18 0.81 1.41 0.97
ARPC3 ENST00000228825 16.32 35.28 23.84 1.48 0.76 1.09 0.81 1.58 1.04
MKRN1 ENST00000255977 16.32 9.75 10.64 1.48 2.44 2.16 0.81 0.50 0.43
HIPK3 ENST00000303296 16.33 16.39 14.06 1.48 1.80 2.04 0.81 0.69 0.60
NR0B1 ENST00000378970 16.33 10.55 11.09 1.48 2.16 2.20 0.81 0.52 0.45
UTP15 ENST00000296792 16.34 1.40 6.14 1.48 3.96 3.21 0.81 0.27 0.30
EIF3B ENST00000360876 16.34 0.38 5.65 1.48 4.12 3.37 0.81 0.28 0.27
LAMTOR4 ENST00000341942 16.35 82.41 48.24 1.48 0.34 0.67 0.81 0.52 1.87
RPL35 ENST00000348462 16.35 38.08 25.30 1.48 0.77 1.05 0.81 1.70 1.16
GPAM ENST00000348367 16.36 35.09 23.79 1.47 0.76 1.11 0.81 1.58 1.03
PLEKHM3 ENST00000427836 16.36 28.05 20.28 1.47 1.19 1.48 0.81 1.19 0.89
EIF2B2 ENST00000266126 16.37 81.12 47.50 1.47 0.35 0.63 0.81 0.55 1.89
EGLN3 ENST00000250457 16.37 50.27 31.53 1.47 0.67 0.86 0.81 1.99 1.56
ADRB2 ENST00000305988 16.38 28.88 20.76 1.47 1.15 1.46 0.82 1.30 0.89
EIF2B3 ENST00000360403 16.38 21.86 16.96 1.47 1.47 1.67 0.82 0.81 0.71
ABCF1 ENST00000326195 16.39 29.38 21.02 1.47 1.10 1.43 0.82 1.36 0.88
ZNF385B ENST00000410066 16.39 40.50 26.57 1.48 0.63 0.99 0.82 1.77 1.25
VPS39 ENST00000318006 16.40 35.88 24.16 1.48 0.80 1.11 0.82 1.58 1.05

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