Human Gene Module / Chromosome 9 / PHF2

PHF2PHD finger protein 2

Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
5 / 5
Rare Variants / Common Variants
6 / 0
Aliases
PHF2, CENP-35,  GRC5,  JHDM1E
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation
Chromosome Band
9q22.31
Associated Disorders
-
Relevance to Autism

Two de novo loss-of-function variants in the PHF2 gene have been identified in ASD probands from the Simons Simplex Collection (refs).

Molecular Function

Lysine demethylase that demethylates both histones and non-histone proteins. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure.

Reports related to PHF2 (5 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary De novo gene disruptions in children on the autistic spectrum. Iossifov I , et al. (2012) Yes -
2 Recent recommendation The contribution of de novo coding mutations to autism spectrum disorder. Iossifov I , et al. (2014) Yes -
3 Recent recommendation Low load for disruptive mutations in autism genes and their biased transmission. Iossifov I , et al. (2015) Yes -
4 Support De novo genic mutations among a Chinese autism spectrum disorder cohort. Wang T , et al. (2016) Yes -
5 Support Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. C Yuen RK , et al. (2017) Yes -
Rare Variants   (6)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.3263delT p.Ile1088fs frameshift_variant De novo - Simplex 22542183 Iossifov I , et al. (2012)
c.2749C>T p.Gln917Ter stop_gained De novo - Simplex 25363768 Iossifov I , et al. (2014)
c.860C>T p.Ala287Val missense_variant Familial Maternal - 27824329 Wang T , et al. (2016)
c.3203-2A>G p.? splice_site_variant Unknown Not maternal - 27824329 Wang T , et al. (2016)
c.860C>T p.Ala287Val missense_variant Unknown - - 27824329 Wang T , et al. (2016)
c.[2963_2964insT(;)2964_2965insCCTCCACCACACCA] p.[Pro988fs(;)p.Pro988fs] frameshift_variant Familial - Simplex 28263302 C Yuen RK , et al. (2017)
Common Variants  

No common variants reported.

SFARI Gene score
3

Suggestive Evidence

Two de novo LoF variants in the PHF2 gene (one frameshift, one nonsense) were identified in ASD probands from the Simons Simplex Collection (PMIDs 22542183, 25363768).

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

CNVs associated with PHF2(1 CNVs)
9q22.31 8 Deletion-Duplication 17  /  80
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