Human Gene Module / Chromosome 5 / GALNT10

GALNT10polypeptide N-acetylgalactosaminyltransferase 10

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
4 / 7
Rare Variants / Common Variants
3 / 6
Aliases
GALNT10, GALNACT10,  PPGALNACT10,  PPGANTASE10
Associated Syndromes
-
Chromosome Band
5q33.2
Associated Disorders
-
Relevance to Autism

A cross-trait meta-analysis of genome-wide association studies on schizophrenia (65,967 cases), bipolar disorder (41,653 cases), autism spectrum disorder (46,350 cases), ADHD (55,374 cases) and depression (688,809 cases) identified an intronic SNP in the GALNT10 gene that reached genome-wide significance for ASD following MTAG analysis (P-value 1.09E-08) (Wu et al., 2020). Another intronic SNP in this gene (rs11740474) has been previously shown to reach genome-wide significance for association with schizophrenia in multiple meta-analyses (Schizophrenia Working Group of the Psychiatric Genomics Consortium, 2014; Li et al., 2017; Ikeda et al., 2019). Two SNPs in GALNT10, including rs11740474, reached genome-wide significance following a combined meta-analysis of GWAS data from the ASD and schizophrenia cohorts of the Psychiatric Genomics Consortium (The Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium 2017).

Molecular Function

This gene encodes a member of the GalNAc polypeptide N-acetylgalactosaminyltransferases. These enzymes catalyze the first step in the synthesis of mucin-type oligosaccharides. These proteins transfer GalNAc from UDP-GalNAc to either serine or threonine residues of polypeptide acceptors.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to GALNT10 (7 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Positive Association Biological insights from 108 schizophrenia-associated genetic loci Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) No -
2 Positive Association Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium (2017) Yes -
3 Positive Association Genome-wide association analysis identifies 30 new susceptibility loci for schizophrenia Li Z et al. (2017) No -
4 Positive Association Genome-Wide Association Study Detected Novel Susceptibility Genes for Schizophrenia and Shared Trans-Populations/Diseases Genetic Effect Ikeda M et al. (2019) No -
5 Primary Multi-trait analysis for genome-wide association study of five psychiatric disorders Wu Y et al. (2020) Yes -
6 Support - Woodbury-Smith M et al. (2022) Yes -
7 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
c.970G>A p.Val324Met missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.828C>T p.Tyr276%3D synonymous_variant De novo - - 35982159 Zhou X et al. (2022)
c.1387-1G>A - splice_site_variant Unknown - - 35205252 Woodbury-Smith M et al. (2022)
Common Variants   (6)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.401+3108A>T - intron_variant - - - 25056061 Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014)
c.401+3108A>T - intron_variant - - - 28540026 Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium (2017)
c.160-34330A>G - intron_variant - - - 28540026 Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium (2017)
c.401+3108A>T - intron_variant - - - 28991256 Li Z et al. (2017)
c.159+30677G>A - intron_variant - - - 32606422 Wu Y et al. (2020)
c.401+3108A>T - intron_variant - - - 30285260 Ikeda M et al. (2019)
SFARI Gene score
2

Strong Candidate

Score Delta: Score remained at 2

criteria met
See SFARI Gene'scoring criteria
2

Strong Candidate

See all Category 2 Genes

We 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
icon
2

Increased from to 2

Krishnan Probability Score

Score 0.32939969886493

Ranking 24989/25841 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.
Original Source
ExAC Score

Score 0.0004492603792158

Ranking 12264/18225 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
Original Source
Sanders TADA Score

Score 0.93760585775876

Ranking 13581/18665 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).
Original Source
Zhang D Score

Score -0.50580048100068

Ranking 19299/20870 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.
Original Source
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