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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
SCT ENST00000176195 93.49 97.08 97.89 0.13 0.24 0.09 0.15 0.19 0.04
RP11-89N17.1 ENST00000311067 93.50 99.60 97.16 0.13 0.16 0.08 0.14 0.12 0.07
AE000662.92 ENST00000557595 93.50 94.07 96.65 0.13 0.25 0.08 0.14 0.26 0.08
AC015989.2 ENST00000593319 93.51 99.61 97.88 0.13 0.16 0.09 0.14 0.12 0.04
AC016757.3 ENST00000409070 93.51 96.61 95.91 0.13 0.23 0.07 0.14 0.20 0.10
RP11-89K11.1 ENST00000560292 93.52 77.85 88.92 0.13 0.42 0.19 0.14 0.79 0.28
C7orf13 ENST00000333319 93.52 99.62 98.48 0.13 0.16 0.10 0.14 0.12 0.05
SPHAR ENST00000366688 93.53 99.62 98.76 0.13 0.16 0.10 0.14 0.12 0.05
ZC2HC1B ENST00000237275 93.53 84.03 91.70 0.13 0.27 0.14 0.14 0.45 0.18
C9orf141 ENST00000371629 93.54 90.90 94.43 0.13 0.25 0.10 0.14 0.35 0.12
NBPF24 ENST00000369228 93.54 93.52 95.03 0.13 0.28 0.09 0.14 0.28 0.10
TSPY2 ENST00000320701 93.55 93.83 96.45 0.13 0.27 0.07 0.14 0.26 0.09
FAM110D ENST00000374268 93.55 53.69 76.64 0.13 0.63 0.37 0.14 1.69 0.61
FAM167B ENST00000373582 93.56 84.64 91.94 0.13 0.27 0.14 0.14 0.42 0.16
OST4 ENST00000456793 93.56 87.04 91.89 0.13 0.22 0.14 0.14 0.40 0.17
WFIKKN1 ENST00000319070 93.57 62.86 80.27 0.13 0.51 0.38 0.14 1.29 0.51
C21orf90 ENST00000330490 93.57 91.52 94.09 0.13 0.23 0.09 0.14 0.32 0.12
SMIM22 ENST00000589327 93.58 95.79 96.22 0.13 0.22 0.07 0.14 0.20 0.09
C1orf220 ENST00000319387 93.59 83.01 90.16 0.13 0.32 0.18 0.14 0.49 0.21
RP11-297M9.1 ENST00000561538 93.59 97.26 97.97 0.13 0.23 0.09 0.14 0.19 0.04
C2CD4D ENST00000454109 93.60 89.72 94.53 0.13 0.27 0.10 0.13 0.37 0.12
AC040160.1 ENST00000454102 93.60 72.10 84.77 0.13 0.52 0.34 0.13 1.04 0.40
BHLHA15 ENST00000609256 93.61 91.66 95.48 0.13 0.24 0.08 0.13 0.32 0.11
C19orf67 ENST00000548523 93.61 53.42 76.69 0.13 0.65 0.35 0.13 1.70 0.60
C17orf50 ENST00000285023 93.62 94.29 95.57 0.13 0.24 0.08 0.13 0.25 0.11

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