Human Gene Module / Chromosome 17 / BPTF

BPTFbromodomain PHD finger transcription factor

SFARI Gene Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
9 / 11
Rare Variants / Common Variants
42 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
17q24.2
Associated Disorders
-
Relevance to Autism

Missense variants in the BPTF gene have been identified in ASD probands from the MSSNG cohort, the SPARK cohort, the Autism Sequencing Consortium, and most recently in a cohort of 75 Turkish patients diagnosed with ASD (Yuen et al., 2017; Zhou et al., 2022; Fu et al., 2022; Kayhan et al., 2026). De novo loss-of-function variants in this gene have been reported in ASD probands from the REACH cohort and a Spanish ASD cohort, as well as in an individual with autism from a ethnically diverse pediatric patient population (Ji et al., 2019; Antaki et al., 2022; Blzquez et al., 2025). ASD has also been reported in a subset of individuals with NEDDFL (2/10 in Stankiewicz et al., 2017, and 3/26 individuals in Glinton et al., 2021).

Molecular Function

This gene was identified by the reactivity of its encoded protein to a monoclonal antibody prepared against brain homogenates from patients with Alzheimer's disease. Analysis of the original protein (fetal Alz-50 reactive clone 1, or FAC1), identified as an 810 aa protein containing a DNA-binding domain and a zinc finger motif, suggested it might play a role in the regulation of transcription. High levels of FAC1 were detected in fetal brain and in patients with neurodegenerative diseases. The protein encoded by this gene is actually much larger than originally thought, and it also contains a C-terminal bromodomain characteristic of proteins that regulate transcription during proliferation. The encoded protein is highly similar to the largest subunit of the Drosophila NURF (nucleosome remodeling factor) complex. In Drosophila, the NURF complex, which catalyzes nucleosome sliding on DNA and interacts with sequence-specific transcription factors, is necessary for the chromatin remodeling

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to BPTF (11 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 Support - Paweł Stankiewicz et al. (2017) No ASD
3 Support - Jianling Ji et al. (2019) Yes -
4 Support Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
5 Support - Kevin E Glinton et al. (2021) No ASD, ADHD
6 Support - Danny Antaki et al. (2022) Yes -
7 Support - Zhou X et al. (2022) Yes -
8 Support - Fu JM et al. (2022) Yes -
9 Support - Ana Blázquez et al. (2025) Yes ADHD, DD
10 Primary - Gülsüm Kayhan et al. (2026) Yes ADHD
11 Support - Wang, Lulu et al. (2026) Yes -
Rare Variants   (42)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.2168G>A p.Arg723His missense_variant De novo - - 35982160 Fu JM et al. (2022)
c.5709-7C>T - splice_region_variant De novo - Simplex 35982159 Zhou X et al. (2022)
c.2779G>A p.Ala927Thr missense_variant Unknown - - 42036727 Wang, Lulu et al. (2026)
c.402G>T p.Glu134Asp missense_variant De novo - Simplex 28263302 C Yuen RK et al. (2017)
c.8081G>C p.Arg2694Thr missense_variant Unknown - - 33522091 Kevin E Glinton et al. (2021)
c.6960A>G p.Ser2320= synonymous_variant De novo - - 31981491 Satterstrom FK et al. (2020)
c.6364A>C p.Thr2122Pro missense_variant De novo - Multiplex 35982159 Zhou X et al. (2022)
c.1282G>T p.Glu428Ter stop_gained De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.8650A>T p.Lys2884Ter stop_gained De novo - - 28942966 Paweł Stankiewicz et al. (2017)
c.2203_2204del p.Arg735fs frameshift_variant De novo - - 35654974 Danny Antaki et al. (2022)
c.2921+1G>C - splice_site_variant Familial Maternal - 33522091 Kevin E Glinton et al. (2021)
c.4555C>T p.Arg1519Ter stop_gained De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.8278G>T p.Glu2760Ter stop_gained De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.3610C>T p.Arg1204Ter stop_gained Familial Maternal - 33522091 Kevin E Glinton et al. (2021)
c.4588C>G p.Gln1530Glu missense_variant Unknown - - 41751633 Gülsüm Kayhan et al. (2026)
c.3360_3370+1del - splice_site_variant De novo - - 28942966 Paweł Stankiewicz et al. (2017)
c.2922-1506_*8577del - copy_number_loss Unknown - - 28942966 Paweł Stankiewicz et al. (2017)
c.5770G>A p.Ala1924Thr missense_variant De novo - - 28942966 Paweł Stankiewicz et al. (2017)
c.8558T>G p.Met2853Arg missense_variant De novo - - 28942966 Paweł Stankiewicz et al. (2017)
c.-121653_2922-3575del - copy_number_loss De novo - - 28942966 Paweł Stankiewicz et al. (2017)
c.8210+6_8210+8del - splice_region_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.486_512del p.Glu162_Asp170del inframe_deletion De novo - Multiplex 35982159 Zhou X et al. (2022)
c.7875+3559_7876-2789del - copy_number_loss De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.1607_1620del p.Asp536GlyfsTer5 frameshift_variant Unknown - - 33522091 Kevin E Glinton et al. (2021)
c.8562_8563del p.Val2855SerfsTer7 frameshift_variant De novo - - 40071278 Ana Blázquez et al. (2025)
c.989del p.Leu330ArgfsTer28 frameshift_variant De novo - - 28942966 Paweł Stankiewicz et al. (2017)
c.2860dup p.Glu954GlyfsTer5 frameshift_variant De novo - - 28942966 Paweł Stankiewicz et al. (2017)
c.3233_3237del p.Arg1078MetfsTer13 frameshift_variant Unknown - - 33522091 Kevin E Glinton et al. (2021)
c.255dupC p.Ser86GlnfsTer43 frameshift_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.2744del p.Asn915ThrfsTer36 frameshift_variant De novo - - 28942966 Paweł Stankiewicz et al. (2017)
c.209dupG p.Ser71GlnfsTer3 frameshift_variant Familial Maternal - 33522091 Kevin E Glinton et al. (2021)
c.255delC p.Ser86AlafsTer151 frameshift_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.6078dup p.Ala2027CysfsTer2 frameshift_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.6259+3_6259+4delinsG p.? splice_region_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.3085delA p.Thr1029GlnfsTer27 frameshift_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.5715_5716delAG p.Val1906GlufsTer15 frameshift_variant De novo - Simplex 30755392 Jianling Ji et al. (2019)
c.2724_2727del p.Thr909SerfsTer4 frameshift_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.5936-1G>A p.Thr1980GlufsTer25 splice_site_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.7521_7524dup p.Leu2509IlefsTer21 frameshift_variant De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.3210_3221del p.Asn1071_Glu1074del inframe_deletion Familial Paternal - 33522091 Kevin E Glinton et al. (2021)
c.(7875+1_7876-1)_(8209+1_8210-1)del - copy_number_loss De novo - Simplex 33522091 Kevin E Glinton et al. (2021)
c.5216_5217del p.Val1739GlyfsTer96 frameshift_variant Unknown Not maternal - 28942966 Paweł Stankiewicz et al. (2017)
Common Variants  

No common variants reported.

SFARI Gene score
3

Suggestive Evidence

criteria met
See SFARI Gene'scoring criteria
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.

4/1/2026
3

Initial score established: 3

Krishnan Probability Score

Score 0.60900141696863

Ranking 270/25841 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 0.99999999999524

Ranking 48/18225 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 0.9499712828023

Ranking 18306/18665 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
Zhang D Score

Score 0.57711876256878

Ranking 144/20870 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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