BPTF

bromodomain PHD finger transcription factor, the group of PHD finger proteins|Bromodomain containing|NURF complex

Basic information

Region (hg38): 17:67825503-67984378

Previous symbols: [ "FALZ" ]

Links

ENSG00000171634

∙ NCBI:2186 ∙ OMIM:601819 ∙ HGNC:3581 ∙ Uniprot:Q12830 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

syndromic intellectual disability (Supportive), mode of inheritance: AD
neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (Strong), mode of inheritance: AD
syndromic intellectual disability (Strong), mode of inheritance: AD
syndromic intellectual disability (Definitive), mode of inheritance: AD
neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Kaposi sarcoma, susceptibility to	AD	Oncologic	Individuals have been described as susceptible to Kaposi sarcoma, and awareness may enable prompt diagnosis and management	Craniofacial; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic	28942966; 33522091; 38380509

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BPTF gene.

not_provided (685 variants)
Inborn_genetic_diseases (291 variants)
Neurodevelopmental_disorder_with_dysmorphic_facies_and_distal_limb_anomalies (113 variants)
BPTF-related_disorder (59 variants)
not_specified (22 variants)
Secondary_microcephaly (8 variants)
Syndromic_intellectual_disability (8 variants)
Expressive_language_delay (8 variants)
Global_developmental_delay (8 variants)
Intellectual_disability (4 variants)
See_cases (4 variants)
Neurodevelopmental_disorder (2 variants)
Kaposi_sarcoma,_susceptibility_to (2 variants)
BPTF-related_neurodevelopmental_disorder (1 variants)
Neurodevelopmental_delay (1 variants)
Microcephaly (1 variants)
Vascular_disorder (1 variants)
Kaposi_sarcoma (1 variants)
Neurodevelopmental_abnormality (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPTF gene is commonly pathogenic or not. These statistics are base on transcript: NM_000182641.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				131 clinvar	20 clinvar	151
missense	1 clinvar	11 clinvar	554 clinvar	96 clinvar	15 clinvar	677
nonsense	9 clinvar	7 clinvar	3 clinvar			19
start loss						0
frameshift	27 clinvar	15 clinvar	4 clinvar			46
splice donor/acceptor (+/-2bp)	1 clinvar	3 clinvar	1 clinvar			5
Total	38	36	562	227	35

Highest pathogenic variant AF is 0.0001590874

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPTF	protein_coding	protein_coding	ENST00000306378	28	158855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.89e-17	125733	0	13	125746	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.71	1067	1.47e+3	0.727	0.0000764	19141
Missense in Polyphen		373	663.19	0.56243		8494
Synonymous	-0.479	547	533	1.03	0.0000284	5675
Loss of Function	10.1	7	133	0.0527	0.00000766	1571

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000224	0.000224
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000278	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Histone-binding component of NURF (nucleosome-remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. May also regulate transcription through direct binding to DNA or transcription factors.;
Disease: DISEASE: Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) [MIM:617755]: An autosomal dominant neurodevelopmental disorder characterized by variable degrees of developmental delay, intellectual disability, speech delay, postnatal microcephaly, dysmorphic features, and mild abnormalities of the hands and feet. {ECO:0000269|PubMed:28942966}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Endoderm Differentiation (Consensus)

Recessive Scores

pRec: 0.131

Intolerance Scores

loftool: 0.278
rvis_EVS: -2.55
rvis_percentile_EVS: 0.86

Haploinsufficiency Scores

pHI: 0.456
hipred: Y
hipred_score: 0.794
ghis: 0.650

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.860

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Bptf
Phenotype: cellular phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype;

Zebrafish Information Network

Gene name: bptf
Affected structure: spinal cord neural keel
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;embryonic placenta development;chromatin remodeling;regulation of transcription by RNA polymerase II;brain development;endoderm development;anterior/posterior pattern specification;positive regulation of transcription by RNA polymerase II
Cellular component: nuclear chromatin;nucleus;nucleoplasm;cytoplasm;NURF complex;Set1C/COMPASS complex;extracellular exosome
Molecular function: protein binding;DNA-dependent ATPase activity;transcription factor binding;methylated histone binding;sequence-specific DNA binding;metal ion binding