Human Gene Module / Chromosome 17 / PHF12

PHF12PHD finger protein 12

High Confidence Criteria 1.1
Autism Reports / Total Reports
2 / 2
Rare Variants / Common Variants
4 / 0
PHF12, PF1
Associated Syndromes
Genetic Category
Rare Single Gene Mutation
Chromosome Band
Associated Disorders
Relevance to Autism

Two de novo protein-truncating variants in the PHF12 gene were identified in ASD probands from the Autism Sequencing Consortium, while an additional protein-truncating variant in this gene was observed in case samples from the Danish iPSYCH study (Satterstrom et al., 2020). TADA analysis of de novo variants from the Simons Simplex Collection and the Autism Sequencing Consortium and protein-truncating variants from iPSYCH in Satterstrom et al., 2020 identified PHF12 as a candidate gene with a false discovery rate (FDR) between 0.01 and 0.05 (0.01 < FDR 0.05). Two de novo variants in the PHF12 gene (one frameshift, one missense) had previously been identified in ASD probands from the Autism Genetics Resource Exchange by whole-genome sequencing in Yuen et al., 2017.

Molecular Function

Acts as a transcriptional repressor. Involved in recruitment of functional SIN3A complexes to DNA. Represses transcription at least in part through the activity of an associated histone deacetylase (HDAC). May also repress transcription in a SIN3A-independent manner through recruitment of functional TLE5 complexes to DNA.

Reports related to PHF12 (2 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder C Yuen RK et al. (2017) Yes -
2 Primary Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.1162C>T p.Gln388Ter stop_gained De novo NA Simplex 31981491 Satterstrom FK et al. (2020)
c.1091dup p.Asn365Ter frameshift_variant De novo NA Simplex 28263302 C Yuen RK et al. (2017)
c.1748G>A p.Arg583Gln missense_variant De novo NA Multiplex 28263302 C Yuen RK et al. (2017)
c.1687dup p.Arg563ProfsTer7 frameshift_variant De novo NA Simplex 31981491 Satterstrom FK et al. (2020)
Common Variants  

No common variants reported.

CNVs associated with PHF12(1 CNVs)
17q11.2 22 Deletion-Duplication 36  /  98
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We are pleased to announce some changes to the ongoing curation of the data in SFARI Gene. In the context of a continued effort to develop the human gene module and its manually curated list of autism risk genes, we are modifying other aspects of the site to focus on the information that is of greatest interest to the research community. The version of SFARI Gene that has been developed until now will be frozen and will remain available as “SFARI Gene Archive”. Please see the announcement for more details.