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Table 1 Cutoffs used to classify affected genes as T1, T2, or T3 candidate driver genes

From: Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

1. Phenotype association

 

Weak

Medium

Strong

 Disease association score (0–5)

pLI > 0.9

RVIS < 10

HI < 10

DDG2P

OMIM

> 0

> 0

> 2

 Total phenomatch score

> 0

> 4

> 10

 Phenomatches (% of HPO terms with phenomatch score > 5)

> 0

> 10%

> 25%

 Mode of inheritance

 

AD/XD/XR+XY

AD/XD/XR+XY

2. Effect of SV on gene

 

Weak

Strong

 Gene location

Adjacent

Dup

Adjacent

DEL/TRUNC

  Support score (0–6)

TAD disrupted

V4C disrupted

PCHiC disrupted

DHS disrupted

RNA expression

> 1

NA

> 3

NA

3. Driver classification

 Classification

T3

T2

T1

  Phenotype association + effect of SV on gene

Weak + weak

Strong + weak

Medium + strong

Strong + strong

  1. pLI probability of being loss-of-function intolerant, RVIS Residual Variation Intolerance Score, HI haploinsufficiency, DDG2P Developmental Disorders Genotype-Phenotype Database, OMIM Online Mendelian Inheritance in Man, AD autosomal dominant, XD X-linked dominant, XR X-linked recessive, XY male, TAD topologically associating domain, V4C virtual 4C, PCHiC promoter capture Hi-C, DHS DNase hypersensitivity site