Human Gene Module / Chromosome 8 / SDC2

SDC2syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan )

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
2 / 4
Rare Variants / Common Variants
1 / 1
Aliases
SDC2, HSPG,  HSPG1,  SYND2
Associated Syndromes
-
Chromosome Band
8q22.1
Associated Disorders
-
Relevance to Autism

Rare mutation in the SDC2 gene has been identified with autism (Ishikawa-Brush et al., 1997).

Molecular Function

The encoded protein is s a transmembrane (type I) heparan sulfate proteoglycan a nd is a member of the syndecan proteoglycan family.

SFARI Genomic Platforms
Reports related to SDC2 (4 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Recent Recommendation Syndecan-2 is expressed in the microvasculature of gliomas and regulates angiogenic processes in microvascular endothelial cells Fears CY , et al. (2006) 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 Primary Autism and multiple exostoses associated with an X;8 translocation occurring within the GRPR gene and 3' to the SDC2 gene Ishikawa-Brush Y , et al. (1997) Yes -
4 Highly Cited Human CASK/LIN-2 binds syndecan-2 and protein 4.1 and localizes to the basolateral membrane of epithelial cells Cohen AR , et al. (1998) No -
Rare Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - translocation - - - 9259269 Ishikawa-Brush Y , et al. (1997)
Common Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.60+25594G>T;c.-28+25882G>T - intron_variant - - - 28540026 Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium (2017)
SFARI Gene score
2

Strong Candidate

Ishikawa-Brush et al., 1997 (PMID: 9259269) showed a translocation breakpoint 30 kb from SDC2.

Score Delta: Score remained at 2

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
3
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2

Decreased from 3 to 2

Description

Ishikawa-Brush et al., 1997 (PMID: 9259269) showed a translocation breakpoint 30 kb from SDC2.

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Ishikawa-Brush et al., 1997 (PMID: 9259269) showed a translocation breakpoint 30 kb from SDC2.

Reports Added
[New Scoring Scheme]
7/1/2014
No data
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4

Increased from No data to 4

Description

Ishikawa-Brush et al., 1997 (PMID: 9259269) showed a translocation breakpoint 30 kb from SDC2.

4/1/2014
No data
icon
4

Increased from No data to 4

Description

Ishikawa-Brush et al., 1997 (PMID: 9259269) showed a translocation breakpoint 30 kb from SDC2.

Krishnan Probability Score

Score 0.45630212155755

Ranking 9905/25841 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 0.57994960090707

Ranking 5091/18225 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 0.90787672838898

Ranking 7255/18665 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 407/461 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 -0.17793533715868

Ranking 14901/20870 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.
Interaction Table
Interactor Symbol Interactor Name Interactor Organism Interactor Type Entrez ID Uniprot ID
CYP2C18 cytochrome P450, family 2, subfamily C, polypeptide 18 Human Protein Binding 1562 P33260
LIPG Endothelial lipase Human Protein Binding 9388 Q9Y5X9
SERPINA1 "<span title=""The name recommended by the UniProt consortium for this chain/part."" class=""tooltipped RECOMMENDED""><a href=""#PRO_0000364030"" onclick=""uniprot.entryViews.openSectionForInternalLink('PRO_0000364030');"">Short peptide from AAT</a>" Human Protein Binding 5265 P01009
SLC7A3 Cationic amino acid transporter 3 Human Protein Binding 84889 Q8WY07
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