FNTB

farnesyltransferase, CAAX box, beta

Basic information

Region (hg38): 14:64986894-65062652

Links

ENSG00000257365 ∙ NCBI:2342 ∙ OMIM:134636 ∙ HGNC:3785 ∙ Uniprot:P49356 ∙ 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 FNTB gene.

• not provided (7 variants)
• Inborn genetic diseases (5 variants)
• not specified (2 variants)
• Hereditary cancer-predisposing syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNTB 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				2	1	3
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding	1			2	3	6
Total	1	0	5	4	4

Highest pathogenic variant AF is 0.0000133

Variants in FNTB

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

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

Position	Type	Phenotype	Significance	ClinVar
14-64986979-A-G		not specified	Uncertain significance (May 08, 2023)
14-64986982-A-G		not specified	Uncertain significance (Sep 27, 2021)
14-64987017-C-T		not specified	Uncertain significance (Apr 28, 2023)
14-64987038-G-A		not specified	Uncertain significance (Feb 16, 2023)
14-64987050-G-C		not specified	Uncertain significance (Sep 20, 2023)
14-64987089-A-T		not specified	Uncertain significance (May 23, 2023)
14-64987090-T-C		not specified	Uncertain significance (Feb 27, 2024)
14-65006156-C-CT			Benign (Aug 10, 2019)
14-65006156-C-CTT			Benign (Aug 09, 2019)
14-65006243-A-C			Pathogenic (Sep 01, 2023)
14-65006289-G-T		Hereditary cancer-predisposing syndrome • Pheochromocytoma • MAX-related disorder	Likely benign (Jan 24, 2023)
14-65006478-G-A			Benign (Jun 15, 2018)
14-65012397-C-A		not specified	Benign (Aug 15, 2023)
14-65032594-G-A		not specified	Likely benign (Aug 15, 2023)
14-65032676-C-T			Likely benign (Jun 01, 2023)
14-65044403-G-A			Likely benign (Jan 01, 2023)
14-65053272-C-T			Benign (Dec 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNTB	protein_coding	protein_coding	ENST00000246166	12	148166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0788	0.921	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	190	252	0.755	0.0000138	2844
Missense in Polyphen		30	88.484	0.33904		1022
Synonymous	-0.659	114	105	1.08	0.00000638	848
Loss of Function	3.43	7	25.8	0.271	0.00000125	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential subunit of the farnesyltransferase complex. Catalyzes the transfer of a farnesyl moiety from farnesyl diphosphate to a cysteine at the fourth position from the C- terminus of several proteins having the C-terminal sequence Cys- aliphatic-aliphatic-X. {ECO:0000269|PubMed:12036349, ECO:0000269|PubMed:12825937, ECO:0000269|PubMed:16893176, ECO:0000269|PubMed:19246009, ECO:0000269|PubMed:8494894}.
• Pathway: Terpenoid backbone biosynthesis - Homo sapiens (human);Signaling by GPCR;Signal Transduction;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.223
• hipred: Y
• hipred_score: 0.553
• ghis: 0.525

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fntb
• Phenotype: immune system phenotype; skeleton phenotype; embryo phenotype; respiratory system 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); hematopoietic system phenotype; growth/size/body region phenotype; neoplasm; cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: fntb
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: negative regulation of cell population proliferation;response to inorganic substance;response to organic cyclic compound;protein prenylation;protein farnesylation;response to cytokine;wound healing;positive regulation of cell cycle;positive regulation of fibroblast proliferation;positive regulation of nitric-oxide synthase biosynthetic process
• Cellular component: cytosol;microtubule associated complex;protein farnesyltransferase complex
• Molecular function: farnesyltranstransferase activity;protein farnesyltransferase activity;protein binding;drug binding;zinc ion binding;isoprenoid binding;peptide binding