FNBP1L

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

Basic information

Region (hg38): 1:93448117-93554661

Previous symbols: [ "C1orf39" ]

Links

ENSG00000137942 ∙ NCBI:54874 ∙ OMIM:608848 ∙ HGNC:20851 ∙ Uniprot:Q5T0N5 ∙ 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 FNBP1L gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNBP1L 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						0
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	18	1	0

Variants in FNBP1L

This is a list of pathogenic ClinVar variants found in the FNBP1L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-93499571-C-G		not specified	Uncertain significance (Feb 26, 2024)
1-93522104-C-G		not specified	Uncertain significance (Aug 22, 2023)
1-93523357-G-A		not specified	Likely benign (Apr 05, 2023)
1-93523379-A-G		not specified	Uncertain significance (Aug 10, 2021)
1-93523471-C-A		not specified	Uncertain significance (May 25, 2022)
1-93529704-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-93529728-C-T		not specified	Uncertain significance (Nov 22, 2023)
1-93530747-G-T			Benign (Jun 23, 2018)
1-93532952-A-G		not specified	Uncertain significance (Jun 18, 2021)
1-93532977-G-C		not specified	Uncertain significance (Jan 23, 2023)
1-93534786-A-G		not specified	Uncertain significance (Sep 27, 2022)
1-93534813-A-C		not specified	Uncertain significance (Jul 20, 2022)
1-93534834-A-T		not specified	Uncertain significance (Feb 06, 2024)
1-93534849-G-A		not specified	Uncertain significance (Sep 26, 2023)
1-93536368-A-C		not specified	Uncertain significance (Oct 25, 2023)
1-93536404-T-G		not specified	Uncertain significance (Jun 02, 2023)
1-93544170-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-93547347-G-A		not specified	Uncertain significance (Nov 22, 2022)
1-93547385-A-T		not specified	Uncertain significance (Dec 01, 2022)
1-93547419-C-G		not specified	Uncertain significance (Aug 10, 2021)
1-93549303-G-A		not specified	Uncertain significance (Jan 10, 2023)
1-93549319-G-A		not specified	Uncertain significance (Jan 18, 2022)
1-93549336-C-G		not specified	Uncertain significance (Oct 29, 2021)
1-93549374-T-G		not specified	Uncertain significance (Aug 13, 2021)
1-93550972-G-C		not specified	Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNBP1L	protein_coding	protein_coding	ENST00000271234	17	106531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.754	0.246	124627	0	13	124640	0.0000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	183	283	0.647	0.0000143	3993
Missense in Polyphen		46	99.649	0.46162		1386
Synonymous	0.288	92	95.6	0.963	0.00000511	999
Loss of Function	4.42	7	35.4	0.198	0.00000193	477

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000543	0.0000531
Middle Eastern	0.00	0.00
South Asian	0.000132	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required to coordinate membrane tubulation with reorganization of the actin cytoskeleton during endocytosis. May bind to lipids such as phosphatidylinositol 4,5-bisphosphate and phosphatidylserine and promote membrane invagination and the formation of tubules. Also promotes CDC42-induced actin polymerization by activating the WASL/N-WASP-WASPIP/WIP complex, the predominant form of WASL/N-WASP in cells. Actin polymerization may promote the fission of membrane tubules to form endocytic vesicles. Essential for autophagy of intracellular bacterial pathogens. {ECO:0000269|PubMed:15260990, ECO:0000269|PubMed:16326391, ECO:0000269|PubMed:19342671}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.487
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.842
• hipred: Y
• hipred_score: 0.696
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fnbp1l
• Phenotype: growth/size/body region phenotype; hearing/vestibular/ear phenotype; skeleton phenotype

Gene ontology

• Biological process: vesicle budding from membrane;autophagy;membrane invagination;vesicle organization;vesicle transport along actin filament;positive regulation of filopodium assembly;cilium assembly;membrane organization;clathrin-dependent endocytosis;plasma membrane tubulation
• Cellular component: cytoplasm;cytosol;cytoskeleton;plasma membrane;cell cortex;cytoplasmic vesicle
• Molecular function: protein binding;lipid binding;cadherin binding;GTPase binding