Human Gene Module / Chromosome 6 / PEX7

PEX7peroxisomal biogenesis factor 7

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
4 / 5
Rare Variants / Common Variants
4 / 2
Aliases
PEX7, RP11-55K22.6,  PTS2R,  RCDP1,  RD
Associated Syndromes
-
Chromosome Band
6q23.3
Associated Disorders
-
Relevance to Autism

Genetic association has been found between the PEX7 gene and ASD in a Korean population cohort (Ro et al., 2012). A homozygous loss-of-function missense variant in the PEX7 gene was identified in three affected children born to consanguineous parents from a multiplex ASD pedigree; this variant was heterozygous in both parents and in three unaffected children (Yu et al., 2013).

Molecular Function

This gene encodes the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2 (PTS2). Defects in this gene cause peroxisome biogenesis disorders (PBDs), which are characterized by multiple defects in peroxisome function.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to PEX7 (5 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Association between peroxisomal biogenesis factor 7 and autism spectrum disorders in a Korean population Ro M , et al. (2012) Yes -
2 Recent Recommendation Using whole-exome sequencing to identify inherited causes of autism Yu TW , et al. (2013) Yes -
3 Support Large-scale discovery of novel genetic causes of developmental disorders Deciphering Developmental Disorders Study (2014) No -
4 Support Genome-wide detection of tandem DNA repeats that are expanded in autism Trost B et al. (2020) Yes -
5 Support - Zhou X et al. (2022) Yes -
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - minisatellite Unknown - Unknown 32717741 Trost B et al. (2020)
c.668T>G p.Leu223Trp missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.225G>C p.Trp75Cys missense_variant Familial Both parents Multiplex 23352163 Yu TW , et al. (2013)
c.883A>G p.Ser295Gly missense_variant De novo - Unknown 25533962 Deciphering Developmental Disorders Study (2014)
Common Variants   (2)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.527-3273G>A;c.413-3273G>A;c.340-6536G>A;c.526+17173G>A A/G intron_variant - - - 22378669 Ro M , et al. (2012)
c.804-11976G>A;c.690-11976G>A;c.510-11976G>A;c.527-11976G>A A/G intron_variant - - - 22378669 Ro M , et al. (2012)
SFARI Gene score
2

Strong Candidate

Genetic association has been found between the PEX7 gene and ASD in a Korean population cohort (Ro et al., 2012). A homozygous loss-of-function missense variant in the PEX7 gene was identified in three affected children born to consanguineous parents from a multiplex ASD pedigree; this variant was heterozygous in both parents and in three unaffected children (Yu et al., 2013).

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
3
icon
2

Decreased from 3 to 2

Description

Genetic association has been found between the PEX7 gene and ASD in a Korean population cohort (Ro et al., 2012). A homozygous loss-of-function missense variant in the PEX7 gene was identified in three affected children born to consanguineous parents from a multiplex ASD pedigree; this variant was heterozygous in both parents and in three unaffected children (Yu et al., 2013).

7/1/2020
3
icon
3

Decreased from 3 to 3

Description

Genetic association has been found between the PEX7 gene and ASD in a Korean population cohort (Ro et al., 2012). A homozygous loss-of-function missense variant in the PEX7 gene was identified in three affected children born to consanguineous parents from a multiplex ASD pedigree; this variant was heterozygous in both parents and in three unaffected children (Yu et al., 2013).

Reports Added
[Genome-wide detection of tandem DNA repeats that are expanded in autism2020]
10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Genetic association has been found between the PEX7 gene and ASD in a Korean population cohort (Ro et al., 2012). A homozygous loss-of-function missense variant in the PEX7 gene was identified in three affected children born to consanguineous parents from a multiplex ASD pedigree; this variant was heterozygous in both parents and in three unaffected children (Yu et al., 2013).

Reports Added
[New Scoring Scheme]
7/1/2018
icon
4

Increased from to 4

Description

Genetic association has been found between the PEX7 gene and ASD in a Korean population cohort (Ro et al., 2012). A homozygous loss-of-function missense variant in the PEX7 gene was identified in three affected children born to consanguineous parents from a multiplex ASD pedigree; this variant was heterozygous in both parents and in three unaffected children (Yu et al., 2013).

Krishnan Probability Score

Score 0.32798561109488

Ranking 25180/25841 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 6.8612830746604E-8

Ranking 15772/18225 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 0.81563175502084

Ranking 2510/18665 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
Larsen Cumulative Evidence Score

Score 16

Ranking 123/461 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.
Original Source
Zhang D Score

Score -0.033856057012926

Ranking 9825/20870 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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