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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
USP17L18 ENST00000504209 91.87 98.64 97.96 0.14 0.20 0.09 0.20 0.15 0.04
KRTAP19-6 ENST00000334046 96.04 99.34 99.37 0.11 0.16 0.11 0.11 0.12 0.04
C9orf53 ENST00000441769 92.84 99.26 97.96 0.15 0.15 0.09 0.16 0.13 0.04
IFNA17 ENST00000413767 96.77 98.50 99.36 0.11 0.21 0.11 0.11 0.15 0.04
ZNF321P ENST00000391777 98.83 92.13 97.95 0.10 0.24 0.09 0.11 0.32 0.04
DEFA3 ENST00000327857 97.10 93.85 97.95 0.10 0.25 0.09 0.11 0.26 0.04
MRPL36 ENST00000508987 96.48 98.82 99.36 0.10 0.16 0.11 0.11 0.14 0.04
AC009892.10 ENST00000456337 94.13 96.79 97.94 0.10 0.23 0.09 0.13 0.19 0.04
ATXN3L ENST00000380622 95.57 99.87 99.35 0.11 0.17 0.11 0.11 0.11 0.04
LAIR2 ENST00000301202 98.77 92.15 97.94 0.10 0.25 0.09 0.11 0.32 0.04
ZNF600 ENST00000338230 97.45 97.90 99.35 0.10 0.20 0.11 0.11 0.17 0.04
C17orf102 ENST00000357754 99.79 91.09 97.93 0.12 0.25 0.09 0.13 0.35 0.04
JSRP1 ENST00000300961 97.35 93.52 97.93 0.10 0.28 0.09 0.11 0.28 0.04
SPN ENST00000360121 99.54 95.92 99.34 0.12 0.22 0.11 0.13 0.20 0.04
DSCR8 ENST00000357704 93.79 97.00 97.92 0.11 0.24 0.09 0.13 0.19 0.04
C10orf25 ENST00000298298 98.91 96.52 99.34 0.10 0.22 0.11 0.11 0.19 0.04
AC127496.1 ENST00000321930 91.64 98.52 97.92 0.14 0.21 0.09 0.20 0.15 0.04
TRIM60 ENST00000512596 97.06 99.26 99.33 0.10 0.15 0.11 0.11 0.13 0.04
AC008060.7 ENST00000401499 96.63 94.19 97.91 0.11 0.25 0.09 0.11 0.25 0.04
TAS2R20 ENST00000538986 96.95 99.87 99.33 0.09 0.17 0.11 0.11 0.11 0.04
CST2 ENST00000304725 94.31 96.48 97.91 0.10 0.22 0.09 0.11 0.19 0.04
VN1R4 ENST00000311170 96.06 99.15 99.32 0.11 0.15 0.11 0.11 0.14 0.04
ZNF114 ENST00000595607 98.59 92.25 97.90 0.10 0.25 0.09 0.11 0.31 0.04
SPATA33 ENST00000301031 95.07 95.71 97.90 0.10 0.23 0.09 0.12 0.20 0.04
HUS1B ENST00000380907 95.67 99.70 99.32 0.11 0.17 0.11 0.11 0.11 0.04

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