Speech/Language Disorders Database

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Gene / phenotype associations for ATP13A4

  • Click column headers to sort. Click to expand any row to see more details about the particular assertion of an association between variants of ATP13A4 and a particular phenotypic variable.
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Entrez Id Symbol Location Disorder Brief Phenotype Reference Year Download
84239 ATP13A4 3q29 SLI Clinically defined expressive and receptive language delay Kwasnicka-Crawford et al 2005 JSON | XML

Basic Study Type:  FISH (flourescence in situ hybridization)

Study Cohort: 
"The proband is a 7-year-old girl with a paracentric inversion, involving 3q25–q29, inherited from her father. The karyotype of proband and father was 46XX, inv(3)(q25–q29) and 46XY, inv(3)(q25–q29), respectively. She was born after an uncomplicated pregnancy and delivered at term. Weight at birth was 7 lb 3 oz. She is shy and quiet and has variability in her social communication skills. At a year and a half of age she had little speech. She started saying words at 2 years of age, phrases at 2 years, 9 months, and sentences when she was in junior kindergarden. Her father was also diagnosed with language delay; he started talking at 4 years of age. There is a family history of late talking as well. At the age of 6 years and 3 months the patient’s nonverbal cognitive abilities were at the 96th percentile, which falls in the high range compared to her same-aged peers. Her total language score was at the 3rd percentile, with an age equivalence of 4 years 1 month. She performed within the low end of the average range in the Communication Domain (19th percentile, age equivalence of 5 years, 7 months), and moderately low range in the Daily Living Skills Domain (12th percentile, age equivalence of 5 years 3 months) and in the Socialization Domain (10th percentile, age equivalence of 4 years 7 months). Overall she performed at the 7th percentile, which is within the moderately low range compared to children her age. On the ADOS scale she exhibited some difficulties in communication and social interaction, with no demonstrated stereotyped behaviors or restricted interests. It was determined clinically that she was not on the autism spectrum and would be most appropriately described as an extremely inhibited child with delayed expressive and receptive language, but age appropriate motor skills."

Genotyping Methods: 
Fluorescence in situ hybridization

"FISH experiments were performed according to standard procedures [39]. Metaphase chromosome spreads were prepared from lymphoblast cell lines established from the father and the proband. The probes used were derived from BACs spanning the 3q25–q29 region and chosen using the UCSC genome browser ( BACs DNA was isolated according to standard protocols (Qiagen) and end-sequenced. Their position on chromosome 3 was confirmed with UCSC Blat. One microgram of DNA was labeled with the Biotin-Nick translation mix or the DIGNick translation mix (Boehringer Mannheim) as described by the supplier. Spreads were then observed on an epifluorescent microscope (Zeiss). The long-range PCR probe was used as an approximate 8-kb probe in narrowing down the distal breakpoint and it was a genomic DNA. Primers for the LRP product were chosen within a hypothetical protein located in that region (AK095277): forward 5'-TCAAGCGTGAATGTTTCTGC-3' and reverse 5'-CTGCCTCCAGTCTCCTCAAC-3'."

RNA isolation and SYBR Green real-time PCR

"Total RNA (2 ig RNA), extracted from patient and normal control lymphoblasts with the RNeasy Mini Kit (Qiagen) and treated with RNase-free DNase (Qiagen) according to the manufacturer’s instructions, was reverse-transcribed into cDNA with Superscript reverse transcriptase (Invitrogen) using oligo(dT) primers followed by PCR using gene-specific primers.

"The expression level of ATP13A4 in patient lymphoblasts was determined by SYBR Green real-time PCR (Applied Biosystems). The theoretical and practical aspects of real-time quantitative RT-PCR using the ABI Prism 7700 sequence detection system (Perkin-Elmer Applied Biosystems) have been described in detail elsewhere [40]. Quantitative values were obtained from the threshold cycle (Ct) number at which the increase in the signal associated with exponential growth of PCR products begins to be detected using PE Biosystems analysis software, according to the manufacture’s manuals. The amount of ATP13A4 transcript was normalized to the GAPDH housekeeping gene, which is ubiquitously expressed. PCR amplifications were always performed in triplicate wells. Primers used for ATP13A4 were chosen within exon 10: ATP13A4, forward primer 5'-TCACCAAAACTCCGTTACCC-3'and reverse primer 5'GTCTGCAGTACCACGGCTCT-3'. Primers for glyceraldehydes-3-phosphate dehydrogenase (GAPDH) were : forward 5'CCTCAACGACCACTTTGTCA-3' and reverse 5'CCCCTCTTCAAGGGGTCTAC-3'. Primers were designed using the Primer3 program ( Parallel PCRs (in triplicates) were conducted with ATP13A4- and GAPDH-specific primers on 1 il of cDNA product that came from the same reverse transcription reaction of the proband or normal control. PCRs were performed using an ABI Prism 7700 sequence detection system and the SYBR Green PCR core reagent kit (Perkin-Elmer Applied Biosystems). The thermal cycling conditions entailed an initial denaturation step at 95deg C for 10 min, followed by 45 cycles at 95deg C for 15 s and 65deg C for 1 min. Results were presented as ratio of ATP13A4 to GAPDH."

Cloning and characterization of human transcripts

"We have searched the GenBank databases for EST sequences overlapping with ATP13A4, a predicted cation-transporting ATPase. Primers designed from the ESTs to isolate a full-length ATP13A4 open-reading frame using RT-PCR are as follows: forward 5'-GGAGGTCATCCTGGAAGC-3', and reverse 5'-GAGTTGTTCTTCATTGCTCTCAAA-3'. Primers used to isolate a full-length ATP13A5
open-reading frame are as follows: forward 5'-GCCCAAGGGATTTTGACAT-3' and reverse 5'-CAGCCTGGCCCAGAAATG-3'. cDNAs were amplified using Pfu polymerase (Stratagene)."

Northern blot analysis

"A multiple-tissue Northern blot containing adult human poly(A)+ RNA (2 ig per lane) was used (Clontech). Probes were labeled with [a-32P]dCTP using random priming. Hybridization and washing were done following manufacturer’s instruction. The cDNA used for probes were exon 27–29 for ATP13A4 (forward primer 5'-TGTCTCCAACTGCTCCAGAA-3' and reverse primer 5'-CCACAAGGGACACAATGAAA-3'), exon 2 for ATP13A5 (forward primer 5'-TGGTTACCGGGACCACAAT-3' and reverse primer 5'-GTTGTCCTCAGCAAAACAGTG-3')."

Mutation screening of ATP13A4

"We analyzed 30 exons of the coding sequence and the splice sites of ATP13A4 by direct sequencing in a sample of 30 probands with autism spectrum disorders. In addition, two healthy controls were included in the analyses. One proband with autism (n = 27) or Asperger syndrome (n = 3) was chosen from every family that contributed to linkage at 3q in the genome-wide screen performed by Auranen et al. [18]. Primers used for mutation screening are available upon request."

Other Details: 
The authors also characterized ATP13A4 in two other ways:
(a) identified the family of proteins it belongs to, and
(b) constructed a phylogenetic tree based on orthologous proteins in various species.

Associated Markers:
D3S3590/D3S2305 breakpoint 


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