Human Gene Module / Chromosome 7 / ST7

ST7suppression of tumorigenicity 7

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
2 / 4
Rare Variants / Common Variants
5 / 0
Aliases
ST7, HELG,  RAY1,  SEN4,  TSG7,  ETS7q,  FAM4A1,  DKFZp762O2113
Associated Syndromes
-
Chromosome Band
7q31.2
Associated Disorders
-
Relevance to Autism

Rare mutation in the ST7 gene has been identified with autism (Vincent et al., 2000).

Molecular Function

The encoded protein is a tumor supressor.

SFARI Genomic Platforms
Reports related to ST7 (4 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Identification of a novel gene on chromosome 7q31 that is interrupted by a translocation breakpoint in an autistic individual Vincent JB , et al. (2000) Yes -
2 Highly Cited Mutational and functional analyses reveal that ST7 is a highly conserved tumor-suppressor gene on human chromosome 7q31 Zenklusen JC , et al. (2001) No -
3 Support Synaptic, transcriptional and chromatin genes disrupted in autism De Rubeis S , et al. (2014) Yes -
4 Support Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families Alazami AM , et al. (2015) No -
Rare Variants   (5)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
T134833C - intron_variant - - - 10889047 Vincent JB , et al. (2000)
T153259C - intron_variant - - - 10889047 Vincent JB , et al. (2000)
- - translocation Familial Maternal - 10889047 Vincent JB , et al. (2000)
c.148A>C p.Thr50Pro missense_variant De novo - - 25363760 De Rubeis S , et al. (2014)
c.489T>G p.Tyr163Ter stop_gained Familial Both parents Multiplex 25558065 Alazami AM , et al. (2015)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

ST7 maps to an autism linkage interval and is disrupted by a translocation in one case.

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

ST7 maps to an autism linkage interval and is disrupted by a translocation in one case.

10/1/2019
4
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3

Decreased from 4 to 3

New Scoring Scheme
Description

ST7 maps to an autism linkage interval and is disrupted by a translocation in one case.

Reports Added
[New Scoring Scheme]
1/1/2015
4
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4

Decreased from 4 to 4

Description

ST7 maps to an autism linkage interval and is disrupted by a translocation in one case.

7/1/2014
No data
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4

Increased from No data to 4

Description

ST7 maps to an autism linkage interval and is disrupted by a translocation in one case.

4/1/2014
No data
icon
4

Increased from No data to 4

Description

ST7 maps to an autism linkage interval and is disrupted by a translocation in one case.

Krishnan Probability Score

Score 0.47830082524861

Ranking 8300/25841 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 0.99805187177665

Ranking 1247/18225 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 0.86101202729301

Ranking 3891/18665 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 409/461 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 -0.19825988703895

Ranking 15384/20870 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
CHRND LRPPRC Human Protein Binding 1144 Q07001
HLA-DQA1 HLA class II histocompatibility antigen, DQ alpha 1 chain Human Protein Binding E9PMV2
ITGB1BP3 integrin beta 1 binding protein 3 Human Protein Binding 27231 Q9NPI5
MYOT myotilin Human Protein Binding 9499 Q9UBF9
PCDHB11 Protocadherin beta-11 Human Protein Binding 56125 Q9Y5F2
PCDHB16 Protocadherin beta-16 Human Protein Binding 57717 Q9NRJ7
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