Table 2

In silico analysis of novel mutations

GeneMutationReference sequenceMutation typeProveanPolyPhen-2Mutation TasterHuman Splicing FinderExAC databaseEvolutionary conservation
B9D1c.508_510delCTC
(p.L170del)		NM_015681IndelDeleterious
(−7.568)		N/ADisease causing
(0.989)		 AbsentCaenorhabditis. elegans
CC2D2Ac.4437+1G>ANM_001080522Splice siteN/AN/AN/ADonor site brokenAbsentPerkinsus. marinus
CEP290c.3777_3778delAG
(p.R1259Sfs*16)		NM_025114Deletion, frameshiftN/AN/ADisease causing
(1.000)		 AbsentDanio rerio
INVSc.1760delA
(p.Q587Rfs*2)		NM_014425Deletion, frameshiftN/AN/ADisease causing
(1.000)		 AbsentXenopus tropicalis
MKS1c.417+1G>ANM_017777Splice siteN/AN/AN/ADonor site brokenAbsentD. rerio
MKS1c.1066C>T
(p.Q356*)		NM_017777NonsenseN/AN/ADisease causing
(1.000)		 AbsentD. rerio
NEK8c.1401G>A
(p.W467*)		NM_178170NonsenseN/AN/ADisease causing
(1.000)		 1 het. allele reported
(MAF=0.000008237)		X. tropicalis
NPHP3c.2694-1_-2delAGNM_153240Deletion, frameshiftN/AN/AN/AAcceptor site broken43 het. alleles reported
(MAF=0.0003553)		D. rerio
PKHD1c.3539G>A
(p.G1180E)		NM_138694MissenseDeleterious
(−6.296)		Probably damaging
(0.999)		Disease causing
(0.761)		 AbsentMus musculus
TCTN2c.252_253delTG
(p.V85Dfs*24)		NM_024809Deletion, frameshiftN/AN/ADisease causing
(1.000)		 AbsentX. tropicalis
TCTN2c.1852C>T
(p.Q618*)		NM_024809NonsenseN/AN/ADisease causing
(1.000)		 AbsentX. tropicalis
TMEM67c.457T>G
(p.C153G)		NM_153704MissenseDeleterious
(−7.289)		Probably damaging
(1.000)		Disease causing
(0.999)		 AbsentC. elegans
TMEM67c.1413-2A>GNM_153704Splice siteN/AN/AN/AAcceptor site brokenAbsentD. rerio

  • Evolutionary conservation at the protein level for non-synonymous changes was analysed by comparing the wild-type amino acid in the human with other orthologues in lower species. The lowest species where exact conservation of amino acid was preserved is shown.

  • Het, heterozygous; MAF, minor allele frequency; N/A, not applicable.