NBPF1

NBPF member 1, the group of NBPF members

Basic information

Region (hg38): 1:16562319-16613562

Links

ENSG00000219481 ∙ NCBI:55672 ∙ OMIM:610501 ∙ HGNC:26088 ∙ Uniprot:Q3BBV0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NBPF1 gene.

• Inborn genetic diseases (10 variants)
• not provided (4 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NBPF1 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				3		3
missense			8	4		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region						0
non coding						0
Total	0	0	10	7	0

Variants in NBPF1

This is a list of pathogenic ClinVar variants found in the NBPF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-16564108-T-A			Likely benign (Oct 01, 2023)
1-16565804-G-A		not specified	Uncertain significance (Mar 25, 2015)
1-16567977-A-G		not specified	Uncertain significance (Mar 25, 2015)
1-16574536-A-G			Likely benign (Jan 01, 2023)
1-16576487-G-T		not specified	Uncertain significance (Mar 25, 2015)
1-16580841-T-A		not specified	Uncertain significance (May 08, 2024)
1-16581450-G-T		not specified	Uncertain significance (Oct 06, 2021)
1-16581452-C-T			Likely benign (Sep 01, 2023)
1-16583686-C-G		not specified	Likely benign (Oct 06, 2021)
1-16583694-A-T			Likely benign (Sep 01, 2023)
1-16587065-C-G		not specified	Uncertain significance (Sep 16, 2021)
1-16587113-T-C		not specified	Uncertain significance (Aug 10, 2021)
1-16589957-C-T		not specified	Uncertain significance (Nov 25, 2024)
1-16589962-C-A		not specified	Uncertain significance (Jul 09, 2024)
1-16589978-T-A		not specified	Uncertain significance (Jul 07, 2022)
1-16589999-A-C		not specified	Uncertain significance (Mar 28, 2024)
1-16591854-C-G		not specified	Likely benign (Jul 06, 2021)
1-16591962-G-C		not specified	Likely benign (Jul 21, 2021)
1-16591967-C-T		not specified	Uncertain significance (Aug 16, 2022)
1-16591980-C-A		not specified	Uncertain significance (Oct 20, 2023)
1-16591999-C-A		not specified	Uncertain significance (Jul 21, 2021)
1-16592006-C-T		not specified	Uncertain significance (Nov 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NBPF1	protein_coding	protein_coding	ENST00000430580	23	51244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.38e-25	0.00288	124850	2	894	125746	0.00357

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.09	485	422	1.15	0.0000205	6361
Missense in Polyphen		155	147.68	1.0495		2322
Synonymous	0.222	156	160	0.978	0.00000868	1637
Loss of Function	0.731	41	46.4	0.884	0.00000235	668

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00371	0.00347
Ashkenazi Jewish	0.00293	0.00288
East Asian	0.00	0.00
Finnish	0.0108	0.0106
European (Non-Finnish)	0.00385	0.00380
Middle Eastern	0.00	0.00
South Asian	0.00282	0.00281
Other	0.00430	0.00424

dbNSFP

Source: dbNSFP

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Cellular component: cytoplasm