Human Gene Module / Chromosome 17 / SLC35B1

SLC35B1solute carrier family 35 member B1

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
0 / 1
Rare Variants / Common Variants
0 / 1
Aliases
SLC35B1, UGTREL1
Associated Syndromes
-
Chromosome Band
17q21.33
Associated Disorders
-
Relevance to Autism

Analysis of genome-wide assocation study (GWAS) data from the Autism Genome Project (AGP) identified two SNPs within the sixth intron of the PHB gene that significantly associated with ADI-R item 69 ('repetitive use of objects or interest in parts of objects'); Hi-C interaction analysis subsequently demonstrated that a 10 kb genomic region containing these two SNPs interacted with an adjacent gene, SLC35B1 (Cantor et al., 2017). Both of these SNPs were significant eQTLs for their candidate target gene SLC35B1 in fetal brains, and one of these SNPs (rs2898883) was significantly associated with thalamic volume (SLC35B1 is strongly expressed in the thalamus from prenatal to postnatal stages of development).

Molecular Function

This gene encodes a nucleotide sugar transporter which is a member of solute carrier family 35. The transporters in this family are highly conserved hydrophobic proteins with multiple transmembrane domains.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
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SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to SLC35B1 (1 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary ASD restricted and repetitive behaviors associated at 17q21.33: genes prioritized by expression in fetal brains Cantor RM , et al. (2017) No -
Rare Variants  

No rare variants reported.

Common Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
- - intergenic_variant - - - 28533516 Cantor RM , et al. (2017)
SFARI Gene score
2

Strong Candidate

Analysis of genome-wide assocation study (GWAS) data from the Autism Genome Project (AGP) identified two SNPs within the sixth intron of the PHB gene that significantly associated with ADI-R item 69 ('repetitive use of objects or interest in parts of objects'); Hi-C interaction analysis subsequently demonstrated that a 10 kb genomic region containing these two SNPs interacted with an adjacent gene, SLC35B1 (Cantor et al., 2017). Both of these SNPs were significant eQTLs for their candidate target gene SLC35B1 in fetal brains, and one of these SNPs (rs2898883) was significantly associated with thalamic volume (SLC35B1 is strongly expressed in the thalamus from prenatal to postnatal stages of development).

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.

10/1/2019
3
icon
2

Decreased from 3 to 2

New Scoring Scheme
Description

Analysis of genome-wide assocation study (GWAS) data from the Autism Genome Project (AGP) identified two SNPs within the sixth intron of the PHB gene that significantly associated with ADI-R item 69 ('repetitive use of objects or interest in parts of objects'); Hi-C interaction analysis subsequently demonstrated that a 10 kb genomic region containing these two SNPs interacted with an adjacent gene, SLC35B1 (Cantor et al., 2017). Both of these SNPs were significant eQTLs for their candidate target gene SLC35B1 in fetal brains, and one of these SNPs (rs2898883) was significantly associated with thalamic volume (SLC35B1 is strongly expressed in the thalamus from prenatal to postnatal stages of development).

Reports Added
[New Scoring Scheme]
4/1/2017
icon
3

Increased from to 3

Description

Analysis of genome-wide assocation study (GWAS) data from the Autism Genome Project (AGP) identified two SNPs within the sixth intron of the PHB gene that significantly associated with ADI-R item 69 ('repetitive use of objects or interest in parts of objects'); Hi-C interaction analysis subsequently demonstrated that a 10 kb genomic region containing these two SNPs interacted with an adjacent gene, SLC35B1 (Cantor et al., 2017). Both of these SNPs were significant eQTLs for their candidate target gene SLC35B1 in fetal brains, and one of these SNPs (rs2898883) was significantly associated with thalamic volume (SLC35B1 is strongly expressed in the thalamus from prenatal to postnatal stages of development).

Krishnan Probability Score

Score 0.47236542985305

Ranking 8799/25841 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 0.013286268594091

Ranking 9786/18225 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 0.81145195198474

Ranking 2423/18665 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 -0.32653015622905

Ranking 17552/20870 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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