BPTF

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

Basic information

Region (hg38): 17:67825502-67984378

Previous symbols: [ "FALZ" ]

Links

ENSG00000171634 ∙ NCBI:2186 ∙ OMIM:601819 ∙ HGNC:3581 ∙ Uniprot:Q12830 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	28942966; 33522091

ClinVar

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

• not provided (429 variants)
• Inborn genetic diseases (88 variants)
• Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (57 variants)
• BPTF-related condition (9 variants)
• not specified (8 variants)
• See cases (4 variants)
• Intellectual disability (3 variants)
• Neurodevelopmental disorder (2 variants)
• Global developmental delay;Secondary microcephaly;Expressive language delay (1 variants)
• Microcephaly;Global developmental delay (1 variants)
• Global developmental delay;Expressive language delay;Secondary microcephaly (1 variants)
• Autism;Joint laxity;Cafe-au-lait spot;Seizure (1 variants)
• Neurodevelopmental delay (1 variants)
• BPTF-related neurodevelopmental disorder (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				71	23	94
missense		4	280	41	18	343
nonsense	3	4	2			9
start loss			1			1
frameshift	14	5	3			22
inframe indel			22	6	4	32
splice donor/acceptor (+/-2bp)			1			1
splice region			4	4	3	11
non coding			4	12	10	26
Total	17	13	313	130	55

Variants in BPTF

This is a list of pathogenic ClinVar variants found in the BPTF region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-67825752-A-C			Uncertain significance (Jul 17, 2023)
17-67825760-C-G		Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies • BPTF-related disorder	Benign/Likely benign (Jan 30, 2024)
17-67825768-CCGCTGCGGAG-C		Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies	Pathogenic (Mar 19, 2020)
17-67825788-C-A		Inborn genetic diseases	Uncertain significance (Dec 09, 2023)
17-67825793-C-T		BPTF-related disorder	Likely benign (Nov 03, 2022)
17-67825793-C-CCCGCCGCCA			Uncertain significance (Aug 17, 2023)
17-67825801-C-T		BPTF-related disorder	Uncertain significance (Oct 20, 2023)
17-67825802-A-G			Likely benign (Oct 22, 2023)
17-67825802-A-ACCGCCG			Conflicting classifications of pathogenicity (Jan 01, 2024)
17-67825816-C-T		Inborn genetic diseases	Uncertain significance (Nov 21, 2023)
17-67825830-A-G			Uncertain significance (Oct 09, 2023)
17-67825833-G-C			Uncertain significance (Jan 15, 2024)
17-67825852-ACCGCGGCAGCAG-A			Uncertain significance (Aug 01, 2022)
17-67825856-C-G			Likely benign (May 08, 2023)
17-67825859-C-T		BPTF-related disorder	Benign/Likely benign (Mar 01, 2024)
17-67825869-G-A		Inborn genetic diseases	Uncertain significance (Jan 16, 2024)
17-67825870-G-C		Inborn genetic diseases	Uncertain significance (May 09, 2023)
17-67825907-G-A			Likely benign (May 26, 2022)
17-67825924-C-T			Uncertain significance (May 18, 2022)
17-67825926-A-AG		Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies • Inborn genetic diseases	Uncertain significance (Jul 27, 2020)
17-67825927-G-C		Inborn genetic diseases	Uncertain significance (Sep 20, 2023)
17-67825929-G-C		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
17-67825930-G-A		BPTF-related disorder	Uncertain significance (Oct 30, 2022)
17-67825930-G-C		Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies • Inborn genetic diseases	Uncertain significance (Jul 14, 2023)
17-67825932-G-T		Inborn genetic diseases	Uncertain significance (Sep 26, 2022)

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