ABAT4-aminobutyrate aminotransferase
Autism Reports / Total Reports
3 / 8Rare Variants / Common Variants
6 / 2Aliases
ABAT, GABAT, NPD009, GABA-AT, GABA transaminaseAssociated Syndromes
-Chromosome Band
16p13.2Associated Disorders
-Relevance to Autism
Genetic association has been found between the ABAT gene and autism in an IMGSAC cohort (Barnby et al., 2005).
Molecular Function
The encoded protein mediates catabolism of GABA into succinic semialdehyde.
External Links
SFARI Genomic Platforms
Reports related to ABAT (8 Reports)
| # | Type | Title | Author, Year | Autism Report | Associated Disorders |
|---|---|---|---|---|---|
| 1 | Primary | Candidate-gene screening and association analysis at the autism-susceptibility locus on chromosome 16p: evidence of association at GRIN2A and ABAT | Barnby G , et al. (2005) | Yes | - |
| 2 | Recent Recommendation | Gabapentin may cause reversible visual field constriction: GABA transaminase inhibitors may cause irreversible visual field loss | Durnian JM and Clearkin LG (2006) | No | - |
| 3 | Highly Cited | Differential effect of gamma-vinyl GABA and valproate on GABA-transaminase from cultured neurones and astrocytes | Larsson OM , et al. (1986) | No | - |
| 4 | Support | Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks | Ruzzo EK , et al. (2019) | Yes | - |
| 5 | Support | - | Zou D et al. (2021) | No | - |
| 6 | Support | - | Zhou X et al. (2022) | Yes | - |
| 7 | Support | - | et al. () | No | Unnamed: 4 |
| 8 | Highly Cited | Measuring human brain GABA in vivo: effects of GABA-transaminase inhibition with vigabatrin | Petroff OA and Rothman DL (1998) | No | - |
Rare Variants (6)
| Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
|---|---|---|---|---|---|---|---|---|
| c.431G>A | p.Arg144Gln | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
| c.928C>T | p.Arg310Trp | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
| c.168+1G>A | - | splice_site_variant | Familial | Both parents | Multiplex | 38177409 | et al. () | |
| c.1004C>T | p.Thr335Met | missense_variant | Familial | Paternal | - | 34145886 | Zou D et al. (2021) | |
| c.1381G>C | p.Gly461Arg | missense_variant | Familial | Maternal | - | 34145886 | Zou D et al. (2021) | |
| c.169-2A>G | - | splice_site_variant | Familial | Paternal | Multiplex | 31398340 | Ruzzo EK , et al. (2019) |
Common Variants (2)
| Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Paternal Transmission | Family Type | PubMed ID | Author, Year |
|---|---|---|---|---|---|---|---|---|
| c.208A>G | p.Gly56Arg | missense_variant | - | - | - | 15830322 | Barnby G , et al. (2005) | |
| c.167A>G;c.221A>G | p.Gln56Arg | missense_variant | - | - | - | 15830322 | Barnby G , et al. (2005) |
SFARI Gene score
2
Strong Candidate
ABAT is a positional candidate from a non-genome-wide significant linkage peak. There is a single study reporting association that does not pass Bonferroni correction.
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
3
2
Decreased from 3 to 2
Description
ABAT is a positional candidate from a non-genome-wide significant linkage peak. There is a single study reporting association that does not pass Bonferroni correction.
10/1/2019
4
3
Decreased from 4 to 3
New Scoring Scheme
Description
ABAT is a positional candidate from a non-genome-wide significant linkage peak. There is a single study reporting association that does not pass Bonferroni correction.
Reports Added
[New Scoring Scheme]7/1/2019
4
4
Decreased from 4 to 4
Description
ABAT is a positional candidate from a non-genome-wide significant linkage peak. There is a single study reporting association that does not pass Bonferroni correction.
7/1/2014
No data
4
Increased from No data to 4
Description
ABAT is a positional candidate from a non-genome-wide significant linkage peak. There is a single study reporting association that does not pass Bonferroni correction.
4/1/2014
No data
4
Increased from No data to 4
Description
ABAT is a positional candidate from a non-genome-wide significant linkage peak. There is a single study reporting association that does not pass Bonferroni correction.
Krishnan Probability Score
Score 0.49199927659389
Ranking 4838/25841 scored genes
[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning
approach on a human brain-specific gene network. The method was first presented in Nat
Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed
in column G of supplementary table 3 (see:
http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser,
with the ability to view networks of associated ASD risk genes, can be found at
asd.princeton.edu.
ExAC Score
Score 0.3743685060483
Ranking 6096/18225 scored genes
[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has
been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by
Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at
exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of-
function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of-
function mutations in autism in such a gene would be more likely to confer risk. For a full list of
pLI scores see:
ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle
aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score
Score 0.84637923639989
Ranking 3337/18665 scored genes
[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013),
and is a statistic that integrates evidence from both de novo and transmitted mutations.
It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233
(2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper
(the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Larsen Cumulative Evidence Score
Score 2
Ranking 372/461 scored genes
[Show Scoring Methodology]
Larsen and colleagues generated gene scores based on the sum of evidence for all available
ASD-associated variants in a gene, with assessments based on mode of inheritance, effect size,
and variant frequency in the general population. The approach was first presented in Mol Autism
7:44 (2016), and scores for 461 genes can be found in column I in supplementary table 4 from
that paper.
Zhang D Score
Score 0.017606647814428
Ranking 8136/20870 scored genes
[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures),
or D score, was developed to combine evidence from de novo loss-of- function mutation with
evidence from cell-type- specific gene expression in the mouse brain (specifically translational
profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with
positive D scores are more likely to be associated with autism risk, with higher-confidence genes
having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204-
215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in
supplementary table 2 from that paper.
External PIN Data
Interactome
- Protein Binding
- DNA Binding
- RNA Binding
- Protein Modification
- Direct Regulation
- ASD-Linked Genes
Interaction Table
| Interactor Symbol | Interactor Name | Interactor Organism | Interactor Type | Entrez ID | Uniprot ID |
|---|---|---|---|---|---|
| ABAT | 4-aminobutyrate aminotransferase | Human | Protein Binding | 18 | P80404 |
| ALDH5A1 | succinic semialdehyde dehydrogenase | Pig | Protein Binding | 100157072 | F1RUE3 |
| ASGR1 | Asialoglycoprotein receptor 1 | Human | Protein Binding | 432 | P07306 |
| BAG3 | BCL2-associated athanogene 3 | Human | Protein Binding | 9531 | O95817 |
| C1ORF228 | Uncharacterized protein C1orf228 | Human | Protein Binding | 339541 | Q6PIY5-2 |
| CHD7 | chromodomain helicase DNA binding protein 7 | Mouse | DNA Binding | 320790 | A2AJK6 |
| CRK | v-crk sarcoma virus CT10 oncogene homolog (avian) | Human | Protein Binding | 1398 | P46108 |
| FMR1 | fragile X mental retardation 1 | Human | RNA Binding | 2332 | G8JLE9 |
| SEC22C | SEC22 vesicle trafficking protein homolog C (S. cerevisiae) | Human | Protein Binding | 9117 | Q9BRL7 |
| SSDH | Succinate-semialdehyde dehydrogenase, mitochondrial | Pig | Protein Binding | 7915 | Q546H9 |
| ZSCAN29 | zinc finger and SCAN domain containing 29 | Human | Protein Binding | 146050 | Q05BJ4 |