Table 3 In silico analyses of novel RECQL variants identified in the study cases from Pakistan

Coding variants

Consensus^a

PolyPhen-2

SIFT

SNAP2

MutationTaster

SNPs&GO

nsSNP Analyzer

c.151G > A (p.E51K)

Benign

Tolerated

Neutral

Disease causing

Neutral

Neutral

Benign

c.421A > T (p.I141F)

Probably damaging

Deleterious

Effect

Disease causing

Disease

Disease

Deleterious (6/6)

c.1651A > G (p.I551V)

Benign

Tolerated

Neutral

Polymorphism

Neutral

Neutral

Benign

Noncoding variants

Consensus^{a, b}

SpliceSiteFinder-like

MaxEntScan

NNSPLICE

GeneSplicer

c.-110G > A

NE

NE

NE

NE

Benign

c.-187 T > G

D (0 → 73.0)

D (0 → 2.9)

NE

NE

Benign

c.215-48C > A

NE

NE

NE

NE

Benign

c.215-37 T > C

NE

NE

NE

NE

Benign

c.700 + 110C > G

NE

NE

NE

NE

Benign

c.868-11G > A

A (0 → 85.8)

A (2.5 → 7.1)

NE

NE

Benign

c.868-2A > G

A (0 → 79.9)^c

A (0 → 5.4)^c

A (0 → 0.4)^c

NE

Deleterious (3/5)

c.949 + 62A > G

NE

NE

NE

NE

Benign

c.1448-18A > G

NE

NE

NE

NE

Benign

c.1667 + 53delT

NE

NE

NE

NE

Benign

c.1668-160C > T

NE

D (2.9 → 1.2)

NE

NE

Benign

c.1668-81G > A

NE

NE

NE

NE

Benign

c.1797 + 14_17delAATT

NE

A (4.8 → 2.3)

NE

NE

Benign