1592G>A. Arg557His. 5.5. 10. ACSL5. 1215C>G. Ile1405Met. 0.2. 16. NPW. 419G>T. Arg140Leu. 0.04. 19. HNRNPUL1. 2005C>A. Gln669Lys. 5.4. 22. MYO18B.
The American Journal of Human Genetics Supplemental Data
Homozygous SLC6A17 Mutations Cause Autosomal-Recessive Intellectual Disability with Progressive Tremor, Speech Impairment, and Behavioral Problems Zafar Iqbal, Marjolein H. Willemsen, Marie-Amélie Papon, Luciana Musante, Marco Benevento, Hao Hu, Hanka Venselaar, Willemijn M. Wissink-Lindhout, Anneke T. Vultovan Silfhout, Lisenka E.L.M. Vissers, Arjan P.M. de Brouwer, Sylviane Marouillat, Thomas F. Wienker, Hans Hilger Ropers, Kimia Kahrizi, Nael Nadif Kasri, Hossein Najmabadi, Frédéric Laumonnier, Tjitske Kleefstra, and Hans van Bokhoven
Figure S1. Molecular modeling (A) Overview structure of SLC6A17. Yellow balls indicate substrate. Grey cylindrical shapes show alpha helices. The magenta color indicates wild type residues Gly162 and Pro633, which are outlined in green and red squares, respectively. (B) Close-up of the p.Gly162Arg mutation. The side chains of both the wild type and the mutant residue are shown and colored green and red, respectively. The mutant residue clashes with helix 4 at position Leu231. (C) Close-up of p.Pro633Arg mutation, showing the side chains of the wild-type (green) and the mutant (red) residue located on an alpha helix on the surface of the protein.
Figure S2. Slc6a17 expression in mouse developmental tissues Slc6a17 mRNA expression was assessed by qPCR using SYBR Green I protocol and arrays containing cDNA from 48 different mouse brain tissues allowing the analysis at five developmental stages (Embryo day 13 (E13), Embryo day 15 (E15), Embryo day 18 (E18), Postnatal day 7 (P7) and Adult week 5 (A5)). Expression of Slc6a17 mRNA is shown relative to Gapdh as a reference gene. The tested regions are Telencephalon (TELEN.), Frontal Cortex (FRONT. CORT.), Posterior Cortex (POST. CORT.), Entorhinal Cortex (ENT. CORT.) Olfactory Bulb (OLFAC. BULB), Hippocampus (HIPP.), Striatum (STRI.), Mesencephalon (MESEN.), Midbrain, Rhombocephalon (RHOMB.), Pons, Medulla (MED.), Cerebellum (CER.), Diencephalon (DIEN.), Thalamus (THAL.), Hypothalamus (HYPO.), Spinal Cord.
Table S1. All private variants identified by exome sequencing in family W10-3099 Chromosome
Gene
cDNA postion
Amino acid position
phyloPa
484G>A
Gly162Arg
6.3
Homozygous variants 1
SLC6A17*
2
IGFBP5
283C>T
His95Tyr
2.4
3
RSRC1
562C>G
Gln188Glu
4.3
7
ZMIZ2
1592G>A
Arg557His
5.5
10
ACSL5
1215C>G
Ile1405Met
0.2
16
NPW
419G>T
Arg140Leu
0.04
19
HNRNPUL1
2005C>A
Gln669Lys
5.4
22
MYO18B
IVS29-1
5.0
Compound heterozygous variants 9
NUP214
283A>G
Ile95Val
-0.04
NUP214
5420G>A
Gly1807Glu
4.9
a
conservation score phyloP *=only variant segregating with the ID phenotype
Table S2. Oligonucleotides used for Slc6a17 RT-PCR analysis and overexpression constructs Primers used for mouse Slc6a17 cloning into pAcGFP1-N In-fusion ready vectors and in vitro mutagenesis Slc6a17-GFPinfus-Fd
AAGGCCTCTGTCGACCACCATGCCGAAGAACAGCAAGGTG
Slc6a17-GFPinfus-Rv
AGAATTCGCAAGCTTCAGCTCTGACTCAGGGGTGC
Slc6a17G162R-Fgt1-Rv
CTCCACCTAATGATCACATTGTAGTACAGCCCA
Slc6a17G162R-Fgt2-Fd
GATCATTAGGTGGAGCGTCTTCTATTTCTTC
Slc6a17P633R-Fgt1-Rv
ACCACACGGATGGGCAGGGTGGCCACGGCAATGAG
Slc6a17P633R-Fgt2-Fd
CCATCCGTGTGGTGTTCATCCTGCGGCACTTCCACT
Primers used for Slc6a17 neurodevelopmental expression analysis Slc6a17-RTqPCR-Fd
ATGTTCACAGTTGGCTGCTG
Slc6a17-RTqPCR-Rv
TCTCAAGGATGACGATGACG
Gapdh-RTqPCR-Fd
CTGCACCACCAACTGCTTAG
Gapdh-RTqPCR-Rv
GTCTTCTGGGTGGCAGTGAT
Table S3. Shared homozygous regions identified in family M328 Sample ID
Chromosome
Start (hg19)
End (hg19)
Length(bp)
M328
chr1
8994112
20572687
11578576
M328
chr1
21448682
27703045
6254364
M328
chr1
103556059
179022650
75466592
M328
chr3
167002413
172011774
5009362
M328
chr3
184467570
189848916
5381347
M328
chr7
57448229
63279469
5831241
M328
chr13
27282769
36453926
9171158
M328
chr16
31905355
46982816
15077462
