PHF3PHD finger protein 3
Autism Reports / Total Reports
2 / 2Rare Variants / Common Variants
6 / 0Aliases
PHF3,Associated Syndromes
-Genetic Category
Rare Single Gene MutationChromosome Band
6q12Associated Disorders
-Relevance to Autism
A de novo loss-of-function (LoF) variant in the PHF3 gene was first identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo LoF variant in this gene was identified by whole genome sequencing in an ASD proband from a multiplex family as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in ASD cases, a probability of LoF intolerance rate (pLI) > 0.9, and a higher-than expected mutation rate (a false discovery rate < 15%), PHF3 was determined to be an ASD candidate gene in Yuen et al., 2017.
Molecular Function
This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development.
Reports related to PHF3 (2 Reports)
# | Type | Title | Author, Year | Autism Report | Associated Disorders |
---|---|---|---|---|---|
1 | Primary | The contribution of de novo coding mutations to autism spectrum disorder. | Iossifov I , et al. (2014) | Yes | - |
2 | Recent Recommendation | 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 |
---|---|---|---|---|---|---|---|---|
3239+CG | 1080-! | frameshift_variant | De novo | - | Simplex | 25363768 | Iossifov I , et al. (2014) | |
c.5758C>T | p.Arg1920Cys | missense_variant | De novo | - | Simplex | 25363768 | Iossifov I , et al. (2014) | |
c.3062_3065del;c.3326_3329del | p.H1021fs;p.His1109fs | frameshift_variant | De novo | - | Multiplex | 28263302 | C Yuen RK , et al. (2017) | |
c.3793C>T;c.4057C>T | p.Arg1265Ter;p.Arg1353Ter | stop_gained | Familial | Maternal | Multiplex | 28263302 | C Yuen RK , et al. (2017) | |
c.2207_2208del | p.Val736fs | frameshift_variant | Familial | Paternal | Multiplex | 28263302 | C Yuen RK , et al. (2017) | |
c.5641_5644del;c.5905_5908del | p.Lys1881fs;p.Lys1969fs | frameshift_variant | Unknown | - | Simplex | 28263302 | C Yuen RK , et al. (2017) |
Common Variants
No common variants reported.
SFARI Gene score
Strong Candidate


2
Score Delta: Increased from 2 to 3.3 + acc
criteria met
See SFARI Gene'scoring criteriaWe 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.
4/1/2018

Increased from 2 to 3.3 + acc
Description
2
4/1/2017

Increased from to 2
Description
A de novo loss-of-function (LoF) variant in the PHF3 gene was first identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo LoF variant in this gene was identified by whole genome sequencing in an ASD proband from a multiplex family as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in ASD cases, a probability of LoF intolerance rate (pLI) > 0.9, and a higher-than expected mutation rate (a false discovery rate < 15%), PHF3 was determined to be an ASD candidate gene in Yuen et al., 2017.
Krishnan Probability Score
Score 0.53192936594763
Ranking 1528/25841 scored genes
[Show Scoring Methodology]
ExAC Score
Score 0.99946941986418
Ranking 942/18225 scored genes
[Show Scoring Methodology]
Iossifov Probability Score
Score 0.964
Ranking 70/239 scored genes
[Show Scoring Methodology]
Sanders TADA Score
Score 0.61972761866288
Ranking 777/18665 scored genes
[Show Scoring Methodology]
Zhang D Score
Score 0.6622942649973
Ranking 8/20870 scored genes
[Show Scoring Methodology]
CNVs associated with PHF3(1 CNVs)
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6q12 | 17 | Deletion-Duplication | 29 / 119 |