FNBP4

formin binding protein 4

Basic information

Region (hg38): 11:47716494-47767443

Links

ENSG00000109920 ∙ NCBI:23360 ∙ OMIM:615265 ∙ HGNC:19752 ∙ Uniprot:Q8N3X1 ∙ 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 FNBP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNBP4 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	3	4
missense			37	1	6	44
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)				1		1
splice region				1		1
non coding				1	1	2
Total	0	0	37	4	11

Variants in FNBP4

This is a list of pathogenic ClinVar variants found in the FNBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47719983-C-T		not specified	Uncertain significance (Jun 11, 2021)
11-47722980-T-C		not specified	Uncertain significance (Dec 15, 2023)
11-47723005-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-47723046-G-C		not specified	Uncertain significance (Jun 23, 2023)
11-47723062-G-T		not specified	Uncertain significance (Dec 13, 2023)
11-47723079-G-A		not specified	Uncertain significance (Dec 02, 2022)
11-47723100-C-T		not specified	Uncertain significance (May 29, 2024)
11-47723140-T-C		not specified	Uncertain significance (Apr 25, 2023)
11-47723200-T-C		not specified	Uncertain significance (Jan 22, 2024)
11-47723235-A-G		not specified	Uncertain significance (Dec 19, 2023)
11-47723238-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-47723260-G-A		not specified	Likely benign (Apr 19, 2023)
11-47723277-A-G		not specified	Uncertain significance (Mar 06, 2023)
11-47723281-C-T		not specified	Uncertain significance (Apr 05, 2023)
11-47724112-T-C			Benign (May 09, 2018)
11-47724144-G-C			Benign (Oct 16, 2019)
11-47724471-G-C		not specified	Uncertain significance (Mar 24, 2023)
11-47724472-C-A			Benign (May 31, 2018)
11-47724472-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-47724512-T-C		not specified	Uncertain significance (Nov 20, 2023)
11-47724592-G-C		not specified	Uncertain significance (Oct 26, 2021)
11-47724616-G-A		not specified	Uncertain significance (Sep 23, 2023)
11-47724774-AGAACCT-A			Likely benign (Dec 31, 2019)
11-47731431-A-C		not specified	Uncertain significance (Oct 06, 2021)
11-47731457-C-G		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNBP4	protein_coding	protein_coding	ENST00000263773	17	50924

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.54e-7	124785	0	8	124793	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	438	528	0.829	0.0000259	6540
Missense in Polyphen		118	186.42	0.63299		2374
Synonymous	-1.41	210	186	1.13	0.00000956	2036
Loss of Function	6.46	3	54.5	0.0551	0.00000306	605

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000265
Middle Eastern	0.000113	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0882

Intolerance Scores

• loftool: 0.141
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.24

Haploinsufficiency Scores

• pHI: 0.526
• hipred: Y
• hipred_score: 0.825
• ghis: 0.537

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fnbp4

Gene ontology

• Cellular component: nuclear speck
• Molecular function: protein binding