FNBP1

formin binding protein 1, the group of F-BAR domain containing

Basic information

Region (hg38): 9:129887187-130043189

Links

ENSG00000187239 ∙ NCBI:23048 ∙ OMIM:606191 ∙ HGNC:17069 ∙ Uniprot:Q96RU3 ∙ 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 FNBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNBP1 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				1	1	2
missense			32	2	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	3	2

Variants in FNBP1

This is a list of pathogenic ClinVar variants found in the FNBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-129895883-C-T		not specified	Uncertain significance (Apr 27, 2024)
9-129895896-A-T		not specified	Uncertain significance (Sep 17, 2021)
9-129895909-C-T		not specified	Uncertain significance (Jun 16, 2024)
9-129895913-T-C		not specified	Uncertain significance (Oct 10, 2023)
9-129895915-C-T		not specified	Uncertain significance (Jan 27, 2022)
9-129895929-G-A		not specified	Likely benign (Jan 20, 2025)
9-129895972-A-G		not specified	Uncertain significance (Feb 26, 2025)
9-129895973-C-T		not specified	Uncertain significance (Dec 03, 2021)
9-129900032-G-A			Benign (Jul 15, 2018)
9-129900042-G-A		not specified	Uncertain significance (Feb 10, 2022)
9-129900091-T-C		not specified	Uncertain significance (Oct 22, 2021)
9-129900095-A-T		not specified	Uncertain significance (Mar 01, 2025)
9-129900442-C-G		not specified	Uncertain significance (Feb 19, 2025)
9-129900442-C-T		not specified	Uncertain significance (Sep 16, 2021)
9-129900459-G-A		not specified	Uncertain significance (May 05, 2022)
9-129900510-C-T		not specified	Uncertain significance (Jan 31, 2025)
9-129900511-G-A		not specified	Uncertain significance (Jun 29, 2022)
9-129900546-G-C			Benign (Jul 15, 2018)
9-129902922-C-T		not specified	Likely benign (Dec 20, 2022)
9-129902923-T-A		not specified	Uncertain significance (Jun 10, 2024)
9-129902937-A-C		not specified	Uncertain significance (Jan 21, 2025)
9-129902949-C-T		not specified	Uncertain significance (Oct 06, 2022)
9-129908989-G-A		not specified	Uncertain significance (Dec 13, 2023)
9-129908990-G-A		not specified	Uncertain significance (Aug 13, 2021)
9-129908991-T-C			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNBP1	protein_coding	protein_coding	ENST00000446176	17	156008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.828	0.172	124632	0	22	124654	0.0000882

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	223	326	0.684	0.0000179	4087
Missense in Polyphen		27	74.552	0.36216		857
Synonymous	0.328	118	123	0.962	0.00000769	1041
Loss of Function	4.54	7	36.6	0.191	0.00000172	473

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000604	0.000604
Ashkenazi Jewish	0.0000999	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000384	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.000203	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a link between RND2 signaling and regulation of the actin cytoskeleton (By similarity). Required to coordinate membrane tubulation with reorganization of the actin cytoskeleton during the late stage of clathrin-mediated endocytosis. Binds to lipids such as phosphatidylinositol 4,5-bisphosphate and phosphatidylserine and promotes membrane invagination and the formation of tubules. Also enhances actin polymerization via the recruitment of WASL/N-WASP, which in turn activates the Arp2/3 complex. Actin polymerization may promote the fission of membrane tubules to form endocytic vesicles. May be required for the lysosomal retention of FASLG/FASL. {ECO:0000250, ECO:0000269|PubMed:15252009, ECO:0000269|PubMed:16318909, ECO:0000269|PubMed:16326391, ECO:0000269|PubMed:16418535, ECO:0000269|PubMed:17512409}.
• Disease: DISEASE: Note=A chromosomal aberration involving FNBP1 is found in acute leukemias. Translocation t(9;11)(q34;q23) with KMT2A/MLL1. The relatively low incidence of the KMT2A/MLL1-FNBP1 fusion protein in acute leukemia may reflect the marginal capacity of this fusion protein to induce cellular transformation.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.164

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.792
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fnbp1

Gene ontology

• Biological process: endocytosis;membrane organization
• Cellular component: lysosome;cytosol;cytoskeleton;plasma membrane;clathrin-coated pit;cell cortex;cytoplasmic vesicle
• Molecular function: protein binding;lipid binding;identical protein binding