Supplementary table 1: In silico analysis, allele frequency in population databases, and variant classification o

Variant (nucleotide change/amino HGVS genomic variant

acid change/) description Exon/ intron
TAOK1 single nucleotide variants

c.70C>A p.(Pro24Thr) NC_000017.11:g.29451618C>A Exon 2

c.170A>C p.(Lys57Thr) NC_000017.11:g.29467182A>C Exon 3

c.306+2T>C NC_000017.11:g.29475773T>C Intron 4

c.427C>T p.(His143Tyr) NC_000017.11:g.29478325C>T Exon 6

c.499C>T p.(Leu167Phe) NC_000017.11:g.29480417C>T Exon 7

c.512G>C p.(Gly171Ala) NC_000017.11:g.29480430G>C Exon 7

c.750-1G>A NC_000017.11:g.29491783G>A Intron 9

c.554C>T p.(Thr185Met) NC_000017.11:g.29480472C>T Exon 7

c.620A>T p.(Asp207Val) NC_000017.11:g.29482253A>T Exon 8

c.627G>A p.(Trp209Ter) NC_000017.11:g.29482260G>A Exon 8

c.656C>T p.(Ala219Val) NC_000017.11:g.29489664C>T Exon 9

c.750G>T p.(Trp250Cys) NC_000017.11:g.29491784G>T Exon 9

c.785T>C p.(Leu262Pro) NC_000017.11:g.29491819T>C Exon 10

c.831+1G>A NC_000017.11:g.29491866G>A Intron 10

c.878T>G p.(Leu293Arg) NC_000017.11:g.29495606T>G Exon 11

c.943dup p.(Leu315ProfsTer8) NC_000017.11:g.29495671dup Exon 11

NC_000017.11:g.29498420_2949
c.1102_1103del p.(Val368Ter) 8421del Exon 12

c.1101T>A p.(Ser367Arg) NC_000017.11:g.29498419T>A Exon 12

c.1101T>A p.(Ser367Arg) NC_000017.11:g.29498419T>A Exon 12

c.1387C>T p.(Gln463Ter) NC_000017.11:g.29507944C>T Exon 14

c.1394_1401dup p. NC_000017.11:g.29507951_2950
(Lys468LeufsTer6) 7958dup Exon 14

c.1414C>T p.(Arg472Ter) NC_000017.11:g.29507971C>T Exon 14

c.1436dup p.(Met479IlefsTer10) NC_000017.11:g.29507993dup Exon 14

c.1813C>T p.(Arg605Ter) NC_000017.11:g.29517561C>T Exon 16
c.1840G>T p.(Glu614Ter) NC_000017.11:g.29517588G>T Exon 16

c.1909-7G>A j NC_000017.11:g.29522273G>A Intron 16

c.1916dup p.(Asn639LysfsTer19) NC_000017.11:g.29522287dup Exon 17

c.2092C>T p.(Arg698Ter) NC_000017.11:g.29522463C>T Exon 17

c.2306C>G p.(Ala769Gly) NC_000017.11:g.29530564C>G Exon 18
c.2410C>T p.(Gln804Ter) NC_000017.11:g.29534166C>T Exon 19
c.2428G>A p.(Glu810Lys) NC_000017.11:g.29534184G>A Exon 19

c.2485C>T p.(Arg829Ter) NC_000017.11:g.29534241C>T Exon 19

c.2593C>T p.(Arg865Ter) NC_000017.11:g.29542609C>T Exon 20

c.2663G>T p.(Ser888Ile) NC_000017.11:g.29542679G>T Exon 20

TAOK1 deletions

NC_000017.11:c.656-3414_832-
895del NC_000017.11:g.29486250_2949
NP_065842.1:p.(Glu220HisfsTer9) 4665del Exon 9-10 (8.42 kb)

chr17:29,343,389-29,462,403x1 NC_000017.11:g. Promoter, Exon 1-2

p.? 29343389_29462403del (119kb)
NC_000017.11:c.-188_655del NC_000017.11:g.29390931_2948
p.? 2288del Exon 1-8 (161.5kb)
chr17:29,512,484-29,543,023x1 NC_000017.11:g.29512484_2954
p.? 3023del Exon 16-20 (30.5kb)
TAOK2 variants

Variant (nucleotide change/amino HGVS genomic variant

acid change) description Exon/ intron
NM_016151.4:c.221_223del p.
(Ile74del)
NC_000016.10:g.29978268_2997
8270del TAOK2α/TAOK2β:Exon 4
NM_016151.4:c.221_223del p.
(Ile74del)
NM_004783.4:c.221_223del p. NC_000016.10:g.29978268_2997
(Ile74del) 8270del TAOK2α/TAOK2β:Exon 4
NM_016151.4:c.463G>A p.
(Gly155Arg)
NM_004783.4:c.463G>A p.
(Gly155Arg) NC_000016.10:g.29979208G>A TAOK2α/TAOK2β:Exon 7
NM_016151.4:c.563+2T>C
NM_004783.4:c.563+2T>C NC_000016.10:g.29979310T>C TAOK2α/TAOK2β: Intron 7
NM_016151.4:c.1260G>A p.
(Pro420=)
NM_004783.4:c.1260G>A p.
(Pro420=) NC_000016.10:g.29983332G>A TAOK2α/TAOK2β:Exon 12
NM_016151.4:c.1496G>A p.
(Arg499Gln)
NM_004783.4:c.1496G>A p.
(Arg499Gln) NC_000016.10:g.29985286G>A TAOK2α/TAOK2β: Exon 14
NM_016151.4:c.1495C>T p.
(Arg499Ter)
NM_004783.4:c.1495C>T p.
(Arg499Ter) NC_000016.10:g.29985285C>T TAOK2α/TAOK2β: Exon 14
NM_016151.4: c.*2906del TAOK2α: Intronic
NM_004783.4: c.2548delC p.
(Arg850GlyfsTer46) NC_000016.10:g.29990886del TAOK2β: Exon 16
NM_016151.4:c.2551del p.
(Val851CysfsTer45) TAOK2α: Exon 16
NM_004783.4:c.2232+319del NC_000016.10:g.29986823del TAOK2β: Intronic
NM_016151.4:c.2811dup p.
(Cys938LeufsTer56) TAOK2α: Exon 16
NM_004783.4:c.2232+579dup NC_000016.10:g.29987083dup TAOK2β: Intronic

Abbreviations: ACMG: American College of Medical Genetics, AF: allele frequency, CC: coiled-coil, LP: likely pathogenic, N
Footnotes:
TAOK1 variants were annotated using the MANE Select transcript NM_020791.4, TAOK2 variants were annotated using the M
Reference sequence IDs for TAOK1 gene: RefSeq Gene (:g.) NC_000017.11 and Protein (:p.) (NP_065842.1)
Reference sequence IDs for TAOK2 gene: RefSeq Gene (:g.) (NC_000016.10) and Protein (:p.) (NP_057235.2) for TAOK2α is
a
REVEL is based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT
b
AlphaMissense is a deep learning model developed by Google DeepMind that categorises single nucleotide missense variants
c
CADD predicts a continuous phred-like score that ranges from 1 to 99, higher values indicating more deleterious variants 6.
d
Metadome tolerance Landscape score: MetaDome analyses the mutation tolerance at each position in a human protein comput
e
SpliceAI predicts whether splicing events occur. The score can range from 0 to 1, when scores can be interpreted as the proba
f
PhyloP (phylogenetic P-values) scores measure evolutionary conservation at individual alignment sites. Interpretations of the
g
DDMut: Predicted Stability Change (ΔΔGStability): Stabilising mutations: (ΔΔG ≥ 0 kcal/mol). Destabilising mutations: (ΔΔ
h
Allele Frequency data from gnomAD: genome data from gnomAD v4.1 11.
i
Allele Frequency data from UK biobank12.
j
Splicing studies showed aberrant splicing with activation of a cryptic splice site resulting in intron inclusion of 5bp, which cre
k
Assessment based on the assumption of a TAOK2 gene-disease association being non-established.
l
Assessment based on the assumption of an established TAOK2 gene-disease association.

Supplementary references:
1- van Woerden GM, Bos M, de Konink C, et al. TAOK1 is associated with neurodevelopmental disorder and essential for
2- Cavalli A, Caraffi SG, Rizzi S, et al. Heterozygous truncating variant of TAOK1 in a boy with periventricular nodular he
3- Kaspi A, Hildebrand MS, Jackson VE, et al. Genetic aetiologies for childhood speech disorder: novel pathways co-expre
4- Ioannidis NM, Rothstein JH, Pejaver V, et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare M
5- Cheng J, Novati G, Pan J, et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science
6- Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pat
7- Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic varian
8- Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, et al. Predicting Splicing from Primary Sequence with Dee
9- Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenie
10- Zhou Y, Pan Q, Pires DEV, Rodrigues CHM, Ascher DB. DDMut: predicting effects of mutations on protein stability usin
11- Chen S, Francioli LC, Goodrich JK, et al. A genomic mutational constraint map using variation in 76,156 human genomes
12- Shuwei Li, Keren J Carss, Bjarni V Halldorsson, Adrian Cortes, UK Biobank Whole-Genome Sequencing Consortium. W
, and variant classification of the TAOK1 and TAOK2 variants reported in the study.

Metadome
Functional domain REVELa Alpha-Missense b CADDc tolerance score d

0.645 0.997 24.8 0.18

PK 0.93 0.999 28.3 0.74

PK N/A N/A 34 N/A

PK 0.897 0.985 23.5 0.28

PK 0.43 0.988 25.4 0.76

PK 0.94 0.997 26.6 0.83

PK N/A N/A 35 N/A

PK 0.83 0.995 26.8 0.55

PK 0.95 0.999 29.7 0.11

PK N/A N/A 38 N/A

PK 0.836 0.988 32 0.19

PK 0.82 0.991 36 0.21

0.936 1 31 0.6

N/A N/A 34 N/A

0.93 0.994 28.6 0.47

SB N/A N/A N/A N/A

SB N/A N/A N/A N/A

SB 0.511 0.996 25.7 0.19

SB 0.511 0.996 25.7 0.19

CC motif 1 N/A N/A 37 N/A

CC motif 1 N/A N/A N/A N/A

CC motif 1 N/A N/A 36 0.2

CC motif 1 N/A N/A N/A N/A

CC motif 2/RD N/A N/A 36 N/A
CC motif 2/RD N/A N/A 40 N/A

CC motif 2/RD N/A N/A 24.5 N/A

CC motif 2/RD N/A N/A N/A N/A

CC motif 2/RD N/A N/A 35 N/A

CC motif 3/ RD 0.37 0.882 31 0.22
CC motif 3/ RD N/A N/A 40 N/A
CC motif 3/ RD 0.49 0.996 32 0.13

CC motif 3/ RD N/A N/A 40 N/A

CC motif 3/ RD N/A N/A 37 N/A

CC motif 3/ RD 0.52 0.897 28.7 0.41

PK N/A N/A N/A N/A

PK N/A N/A N/A N/A

PK N/A N/A N/A N/A

CC motifs 1-3/ RD N/A N/A N/A N/A

Metadome
Functional domain REVELa Alpha-Missense b CADDc tolerance score d

PK N/A N/A N/A 0.38

 PK N/A N/A N/A 0.38

PK 0.53 1 32 0.16

N/A N/A 35 N/A

CC motif 1 N/A N/A 24.8 N/A

CC motif 1 0.41 0.909 31 0.87

CC motif 1 N/A N/A 36 N/A

RD N/A N/A N/A N/A

RD N/A N/A N/A N/A

RD N/A N/A N/A N/A

iled-coil, LP: likely pathogenic, N/A: not applicable/available, P: pathogenic, PK: Protein kinase, RD: regulatory domain, SB: Substrate‐bin

iants were annotated using the MANE Select NM_016151.4 transcript for TAOK2α isoform and the NM_004783.4 for TAOK2β isoform.
(NP_065842.1)
) (NP_057235.2) for TAOK2α isoform and (NP_004774.1) for TAOK2β isoform.
2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. It range
gle nucleotide missense variants as either likely pathogenic or likely benign. For each missense variant, the 'am_pathogenicity' and 'am_cla
ng more deleterious variants 6.
sition in a human protein computed as non-synonymous over synonymous ratio to quantify genetic tolerance, in a sliding window (with a si
s can be interpreted as the probability of the variant being splice-altering 8.
ment sites. Interpretations of the scores are compared to the evolution that is expected under neutral drift. Positive scores indicate slower ev
ol). Destabilising mutations: (ΔΔG < 0 kcal/mol) 10.

ntron inclusion of 5bp, which creates a frameshift, with the transcript predicted to undergo nonsense mediated decay.

mental disorder and essential for neuronal maturation and cortical development. Hum Mutat. 2021;42(4):445-459. doi:10.1002/humu.24176
y with periventricular nodular heterotopia: a case report and literature review of TAOK1-related neurodevelopmental disorders. BMC Med
sorder: novel pathways co-expressed during brain development [published correction appears in Mol Psychiatry. 2023 Apr;28(4):1664-166
ting the Pathogenicity of Rare Missense Variants. Am J Hum Genet. 2016;99(4):877-885. doi:10.1016/j.ajhg.2016.08.016
ion with AlphaMissense. Science. 2023;381(6664):eadg7492. doi:10.1126/science.adg7492
ork for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46(3):310-315. doi:10.1038/ng.2892
enicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat. 2019;40(8):1030-1038. doi:10
rom Primary Sequence with Deep Learning. Cell. 2019;176(3):535-548.e24. doi:10.1016/j.cell.2018.12.015
rates on mammalian phylogenies. Genome Res. 2010;20(1):110-121. doi:10.1101/gr.097857.109
mutations on protein stability using deep learning. Nucleic Acids Res. 2023;51(W1):W122-W128. doi:10.1093/nar/gkad472
riation in 76,156 human genomes [published correction appears in Nature. 2024 Feb;626(7997):E1]. Nature. 2024;625(7993):92-100. doi:1
ome Sequencing Consortium. Whole-genome sequencing of half-a-million UK Biobank participants. medRxiv 2023.12.06.23299426; doi:
 DDMut: Predicted
Stability Change gnomAD 4.0 allele UK biobank allele
Splice AI e phyloP f (ΔΔGStability) g frequency h frequency i

-2.78 kcal/mol
Benign (0) 7.893 Destabilising) Absent Absent
-1.61 kcal/mol
Benign (0) 9.325 (Destabilising) Absent Absent
Donor Loss 0.98
Donor Gain 0.61 8.01 N/A Absent Absent

-0.74 kcal/mol
Benign (0) 7.905 (Destabilising) Absent Absent

-0.96 kcal/mol
Benign (0) 6.1 (Destabilising) Absent Absent
-0.17 kcal/mol
Benign (0) 9.905 (Destabilising) Absent Absent
Acceptor loss 0.99 9.923 N/A Absent Absent
-0.71 kcal/mol
Benign (0.03) 7.831 (Destabilising) Absent Absent
-0.89 kcal/mol
Benign (0) 9.234 (Destabilising) Absent Absent
Benign (0) 9.904 N/A Absent Absent
0.49 kcal/mol 4/1446728 AF
Benign (0.01) 7.834 (Stabilising) 0.000002765 3/981074 AF 3.06e-6

Acceptor Loss 0.72 -0.66 kcal/mol

Acceptor gain 0.26 9.923 (Destabilising) Absent Absent
-2.45 kcal/mol
Benign (0) 7.955 (Destabilising) Absent Absent

Donor Loss 0.99

Acceptor Loss 0.89 10.003 N/A Absent Absent
-1.69 kcal/mol
Benign (0) 7.898 (Destabilising) Absent Absent

Benign (0.01) 1.928 N/A Absent Absent

Benign (0) 7.508 N/A Absent Absent

Benign (0) 1.732 N/A Absent Absent

Benign (0) 1.732 N/A Absent Absent

Benign (0) 7.9 N/A Absent Absent

Benign (0.02) 8.086 N/A Absent Absent

Benign (0) 1.668 N/A Absent Absent

Benign (0) 9.32 N/A Absent Absent

Benign (0) 1.058 N/A Absent Absent
Benign (0) 8.123 N/A Absent Absent

Acceptor Gain 1.00

Acceptor Loss 0.62 1.976 N/A Absent Absent

Benign (0.01) 8.005 N/A Absent Absent

Benign (0) 1.563 N/A Absent Absent

Donor Gain 0.6 7.9 N/A Absent Absent
Benign (0) 7.905 N/A Absent Absent
Benign (0) 10.003 N/A Absent Absent
1/1460812 AF
Benign (0) 5.014 N/A 6.846e-7 Absent

Benign (0.02) 4.908 N/A Absent Absent

Benign (0.02) 10.003 N/A Absent Absent

N/A N/A N/A N/A N/A

N/A N/A N/A N/A N/A

N/A N/A N/A N/A N/A

N/A N/A N/A N/A N/A

DDMut: Predicted
Stability Change gnomAD 4.0 allele UK biobank allele
Splice AI e phyloP f (ΔΔGStability) g frequency h frequency i

Benign (0) 9.325 N/A Absent Absent

 Benign (0) 9.325 N/A Absent Absent

0.22 kcal/mol
Benign (0) 9.917 (Stabilising) Absent Absent

Donor Loss 0.98

Donor Gain 0.91 7.931 N/A Absent Absent

4/1441368 AF 1/917678 AF
Donor Loss 0.80 2.731 N/A 0.000002775 0.00000109

Benign (0) 10.003 N/A Absent Absent

1/1596674 AF
Benign (0) 2.619 N/A 6.263e-7 Absent

Benign (0) 0.82 N/A Absent Absent

Benign (0) 1.491 N/A Absent Absent

Benign (0) -0.311 N/A Absent Absent

e, RD: regulatory domain, SB: Substrate‐binding, VUS: variant of uncertain significance

d the NM_004783.4 for TAOK2β isoform.

P++, SiPhy, phyloP, and phastCons. It ranges from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing
variant, the 'am_pathogenicity' and 'am_class' are displayed. The 'am_pathogenicity' is a continuous score between 0 and 1 and can be inte

etic tolerance, in a sliding window (with a size of 21 codons/residues) to provide a per-position indication of regional tolerance to missense

utral drift. Positive scores indicate slower evolution than expected (conserved nucleotides) and negative scores indicate nucleotides that are
ense mediated decay.

21;42(4):445-459. doi:10.1002/humu.24176
d neurodevelopmental disorders. BMC Med Genomics. 2024;17(1):68. doi:10.1186/s12920-024-01840-8
n Mol Psychiatry. 2023 Apr;28(4):1664-1666. doi: 10.1038/s41380-022-01879-y]. Mol Psychiatry. 2023;28(4):1647-1663. doi:10.1038/s41
0.1016/j.ajhg.2016.08.016

10-315. doi:10.1038/ng.2892
. Hum Mutat. 2019;40(8):1030-1038. doi:10.1002/humu.23798
2018.12.015

28. doi:10.1093/nar/gkad472
:E1]. Nature. 2024;625(7993):92-100. doi:10.1038/s41586-023-06045-0
pants. medRxiv 2023.12.06.23299426; doi: https://doi.org/10.1101/2023.12.06.23299426
ClinVar (Variation Reported in
ID/ Pathogenicity) literature Pathogenicity criteria

N/A Not reported PM2 PS2_sup = VUS

N/A Not reported PM2 PM1 PP3 PM6_sup = LP

N/A Not reported PM2 PVS1_strong = LP

N/A Not reported PM2 PP3 PM1 PS2_sup = LP

N/A Not reported PM2 PM1 = VUS

N/A Not reported PM2 PP3 PM1 = VUS

N/A Not reported PM2 PVS1 = VUS

N/A Not reported PM2 PM1 PP3 = VUS

1311193/VUS Not reported PM2 PM5_sup PP3 PM1 PS4_sup = LP

N/A Not reported PM2 PVs1 = P

N/A Not reported PM1_sup PS2_sup PP3 = VUS

N/A Not reported PM2 PP3 PM1 PP2 = LP

N/A Not reported PM2 PP3 PM1_sup PS2_mod = LP

N/A Not reported PVS1 PM2 PM6 = P

N/A Not reported PM2 PP3 PP2 PM6 = LP

N/A Not reported PM2 PVs1 = P

N/A Not reported PM2 PVs1 = P

2503239/VUS Not reported PM2 PP2 = VUS

2503239/VUS Not reported PM2 PP2 = VUS

N/A Not reported PVS1 PM6_sup = LP

N/A Not reported PM2 PVs1 = P

2632425/LP Reported2 PVS1 PM2 = P

1701871/LP Not reported PM2 PVs1 = P

1879365/P Reported1 PM2 PVS1 PS4_mod = P
N/A Not reported PM2 PVs1 = P

N/A Not reported PM2 PVS1_str(RNA) PS2_mod = LP

2502349/LP Not reported PM2 PVs1 = P

1333401/LP Not reported PM2 PVs1 = P

N/A Not reported PM2 PP3 = P
N/A Not reported PM2 PVS1 PS2_sup = P
N/A Not reported BP5 = VUS

N/A Not reported PVS1 = VUS

N/A Not reported PM2 PVS1str = P

N/A Not reported PM2 PS2_mod = VUS

N/A Not reported PM2 PVS1 = P

N/A Not reported PVS1 + PM2 + PM6 = P

N/A Not reported PM2 PVS1 = P

N/A Not reported PM2 PVS1_str PM4_sup = LP

ClinVar (Variation Reported in Pathogenicity

ID/ Pathogenicity) literature criteria k Pathogenicity criteria l

PM2 PM1 PM2 PM1 PM4_sup =

N/A Not reported PM4_sup = VUS VUS
 PM2 PM1 PM2 PM1 PM4_sup =
N/A Not reported PM4_sup = VUS VUS

2102347/VUS Not reported PM2 PM1 = VUS PM2 PM1 = VUS

N/A Not reported PM2 PP3 = VUS PM2 PVS1_strong = LP

PP3 PS2_sup =
N/A Not reported VUS PP3 PS2_sup = VUS

The individual is PM2 PS2_sup =

N/A reported as P12 3 VUS PM2 PS2_sup = VUS

N/A Not reported PM2 = VUS PM2 PVS1 = P

PM2 PS2_sup = PM2 PS2_sup

N/A Not reported VUS PVS1_strong = LP

N/A Not reported PM2 = VUS PM2 PVS1_strong = LP

1502376/VUS Not reported VUS PVS1_strong = VUS

that the variant is disease-causing 4.

e between 0 and 1 and can be interpreted as the predicted probability of the variant being pathogenic. The 'am_class' is the classification of

n of regional tolerance to missense variation. Scores <0.7 are considered intolerant. Slightly intolerant ≤ 0.7. Intolerant ≤ 0.525. Highly into

cores indicate nucleotides that are predicted to be fast-evolving 9.

28(4):1647-1663. doi:10.1038/s41380-022-01764-8
ass' is the classification of the variant into one of three discrete categories, 'Likely pathogenic' (>0.564), 'Likely benign' (<0.34), or 'ambigu

lerant ≤ 0.525. Highly intolerant ≤ 0.17577.

nign' (<0.34), or 'ambiguous' (0.34 – 0.564) 5.