NIPA2non imprinted in Prader-Willi/Angelman syndrome 2
Autism Reports / Total Reports
3 / 3Rare Variants / Common Variants
3 / 0Aliases
-Associated Syndromes
-Chromosome Band
15q11.2Associated Disorders
IDRelevance to Autism
A rare NIPA2 deletion was found in a patient with PDD-NOS and mild intellectual disability (Leblond et al., 2012).
Molecular Function
This gene encodes a possible magnesium transporter. This gene is located adjacent to the imprinted domain in the Prader-Willi syndrome deletion region of chromosome 15. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 7 and 21.
External Links
SFARI Genomic Platforms
Reports related to NIPA2 (3 Reports)
# | Type | Title | Author, Year | Autism Report | Associated Disorders |
---|---|---|---|---|---|
1 | Support | A co-segregating microduplication of chromosome 15q11.2 pinpoints two risk genes for autism spectrum disorder | van der Zwaag B , et al. (2009) | Yes | - |
2 | Primary | Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders | Leblond CS , et al. (2012) | Yes | ID |
3 | Support | - | Zhou X et al. (2022) | Yes | - |
Rare Variants (3)
Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
---|---|---|---|---|---|---|---|---|
- | - | copy_number_loss | Familial | Paternal | Simplex | 22346768 | Leblond CS , et al. (2012) | |
c.432C>G | p.His144Gln | missense_variant | De novo | - | Simplex | 35982159 | Zhou X et al. (2022) | |
- | - | copy_number_gain | Familial | Paternal | Multi-generational | 20029941 | van der Zwaag B , et al. (2009) |
Common Variants
No common variants reported.
SFARI Gene score
Strong Candidate
NIPA2 is one of four genes that resides within the 15q11.2 CNV locus, a chromosomal region between breakpoints 1 (BP1) and 2 (BP2) of the Prader-Willi/Angelman syndrome critical region in which deletions and duplications are associated with increased susceptibility to neurodevelopmental disorders, including autism (van der Zwaag et al., 2010; Leblond et al., 2012).
Score Delta: Score remained at 2
criteria met
See SFARI Gene'scoring criteriaWe considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.
4/1/2022
Decreased from 3 to 2
Description
NIPA2 is one of four genes that resides within the 15q11.2 CNV locus, a chromosomal region between breakpoints 1 (BP1) and 2 (BP2) of the Prader-Willi/Angelman syndrome critical region in which deletions and duplications are associated with increased susceptibility to neurodevelopmental disorders, including autism (van der Zwaag et al., 2010; Leblond et al., 2012).
10/1/2019
Decreased from 4 to 3
New Scoring Scheme
Description
NIPA2 is one of four genes that resides within the 15q11.2 CNV locus, a chromosomal region between breakpoints 1 (BP1) and 2 (BP2) of the Prader-Willi/Angelman syndrome critical region in which deletions and duplications are associated with increased susceptibility to neurodevelopmental disorders, including autism (van der Zwaag et al., 2010; Leblond et al., 2012).
Reports Added
[New Scoring Scheme]10/1/2017
Increased from to 4
Description
NIPA2 is one of four genes that resides within the 15q11.2 CNV locus, a chromosomal region between breakpoints 1 (BP1) and 2 (BP2) of the Prader-Willi/Angelman syndrome critical region in which deletions and duplications are associated with increased susceptibility to neurodevelopmental disorders, including autism (van der Zwaag et al., 2010; Leblond et al., 2012).
Krishnan Probability Score
Score 0.4490718568878
Ranking 11305/25841 scored genes
[Show Scoring Methodology]
ExAC Score
Score 0.48719375365062
Ranking 5520/18225 scored genes
[Show Scoring Methodology]
Sanders TADA Score
Score 0.8950968507404
Ranking 5927/18665 scored genes
[Show Scoring Methodology]
Zhang D Score
Score -0.11400718603516
Ranking 12897/20870 scored genes
[Show Scoring Methodology]
CNVs associated with NIPA2(1 CNVs)
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15q11.2 | 122 | Deletion-Duplication | 161 / 2259 |