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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
ING5 ENST00000313552 3.75 21.02 9.93 3.79 1.43 2.29 0.30 0.83 0.42
ZCCHC11 ENST00000257177 3.75 1.31 0.88 3.79 3.97 4.50 0.30 0.27 0.20
FAF2 ENST00000261942 3.76 4.09 1.79 3.79 3.25 4.23 0.30 0.32 0.23
INO80 ENST00000361937 3.77 0.10 0.56 3.78 4.12 4.71 0.30 0.28 0.17
CAB39 ENST00000258418 3.77 23.21 11.14 3.78 1.43 2.19 0.30 0.91 0.45
NAA30 ENST00000556492 3.78 7.29 2.92 3.78 2.58 3.99 0.30 0.37 0.23
TAOK3 ENST00000392533 3.78 8.23 3.45 3.78 2.58 3.85 0.30 0.45 0.23
ZFR ENST00000265069 3.79 2.16 1.15 3.77 3.66 4.43 0.30 0.29 0.21
ZNF131 ENST00000509634 3.79 3.45 1.59 3.77 3.40 4.28 0.30 0.29 0.23
ZNF281 ENST00000294740 3.80 8.32 3.49 3.77 2.52 3.85 0.30 0.45 0.23
MED12 ENST00000374080 3.80 0.17 0.58 3.77 4.11 4.70 0.30 0.28 0.17
RAB11B ENST00000328024 3.81 33.55 16.52 3.77 0.85 1.71 0.30 1.53 0.69
ANKRD13B ENST00000394859 3.81 20.49 9.60 3.76 1.43 2.28 0.30 0.78 0.40
NKX2-5 ENST00000329198 3.82 14.26 6.35 3.76 2.06 3.09 0.30 0.61 0.32
IPO13 ENST00000372343 3.82 5.87 2.46 3.76 2.85 4.02 0.30 0.35 0.23
SEC61A2 ENST00000298428 3.83 29.07 14.16 3.77 1.13 2.00 0.30 1.32 0.60
SF3B14 ENST00000233468 3.83 35.08 17.32 3.77 0.76 1.63 0.30 1.58 0.75
NACC1 ENST00000292431 3.84 4.61 1.99 3.77 3.25 4.11 0.30 0.32 0.23
HNRNPDL ENST00000295470 3.84 22.21 10.62 3.76 1.53 2.16 0.30 0.81 0.43
SSRP1 ENST00000278412 3.85 10.22 4.29 3.78 2.29 3.75 0.30 0.49 0.24
NCBP1 ENST00000375147 3.85 0.92 0.79 3.77 4.11 4.55 0.30 0.29 0.21
PRPF18 ENST00000378572 3.86 44.12 22.10 3.77 0.61 1.15 0.30 1.97 0.96
ABHD17C ENST00000258884 3.86 14.60 6.61 3.77 2.04 3.00 0.30 0.61 0.32
CFLAR ENST00000309955 3.87 3.90 1.77 3.77 3.29 4.23 0.30 0.31 0.23
MAU2 ENST00000392313 3.87 1.77 1.05 3.77 3.81 4.43 0.30 0.26 0.21

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