FNTA

farnesyltransferase, CAAX box, alpha, the group of Prenyltransferase alpha subunit repeat containing

Basic information

Region (hg38): 8:43034194-43085788

Links

ENSG00000168522 ∙ NCBI:2339 ∙ OMIM:134635 ∙ HGNC:3782 ∙ Uniprot:P49354 ∙ 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 FNTA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNTA 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
missense			25		1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	2

Variants in FNTA

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

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

Position	Type	Phenotype	Significance	ClinVar
8-43056359-G-A		not specified	Uncertain significance (Oct 05, 2021)
8-43056362-G-T		not specified	Uncertain significance (Jun 28, 2022)
8-43056365-G-T		not specified	Uncertain significance (Jul 13, 2022)
8-43056368-G-A		not specified	Uncertain significance (Nov 13, 2023)
8-43056387-G-A		not specified	Uncertain significance (Jan 12, 2024)
8-43056498-T-C		not specified	Uncertain significance (Aug 02, 2023)
8-43056503-G-C		not specified	Uncertain significance (Oct 27, 2021)
8-43056528-C-T		not specified	Uncertain significance (Jul 25, 2023)
8-43056536-G-A			Benign (Mar 29, 2018)
8-43059115-T-C		not specified	Uncertain significance (Aug 14, 2023)
8-43064143-A-G		not specified	Uncertain significance (May 23, 2023)
8-43064165-T-G		not specified	Uncertain significance (Jan 23, 2024)
8-43064173-C-G		not specified	Uncertain significance (Mar 25, 2024)
8-43064176-G-A		not specified	Uncertain significance (Feb 05, 2025)
8-43069556-C-T		not specified	Uncertain significance (Oct 03, 2023)
8-43069580-T-A		not specified	Uncertain significance (Jan 17, 2024)
8-43069625-A-G		not specified	Uncertain significance (Oct 27, 2023)
8-43069647-A-C		not specified	Uncertain significance (Dec 30, 2024)
8-43072234-A-C		not specified	Uncertain significance (Sep 03, 2024)
8-43072249-T-C		not specified	Uncertain significance (Oct 12, 2021)
8-43077236-T-G		not specified	Uncertain significance (Aug 16, 2022)
8-43077309-G-A		not specified	Uncertain significance (Dec 27, 2023)
8-43083120-A-G		not specified	Uncertain significance (Jan 31, 2023)
8-43083128-G-A		not specified	Uncertain significance (Nov 29, 2023)
8-43083147-C-T		not specified	Uncertain significance (Aug 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNTA	protein_coding	protein_coding	ENST00000302279	9	51595

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.947	0.0528	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.804	158	189	0.836	0.00000953	2477
Missense in Polyphen		29	58.963	0.49183		771
Synonymous	-0.607	75	68.6	1.09	0.00000335	663
Loss of Function	3.81	3	22.5	0.133	0.00000120	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000624	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential subunit of both the farnesyltransferase and the geranylgeranyltransferase complex. Contributes to the transfer of a farnesyl or geranylgeranyl moiety from farnesyl or geranylgeranyl diphosphate to a cysteine at the fourth position from the C-terminus of several proteins having the C-terminal sequence Cys-aliphatic-aliphatic-X. May positively regulate neuromuscular junction development downstream of MUSK via its function in RAC1 prenylation and activation. {ECO:0000269|PubMed:12036349, ECO:0000269|PubMed:12825937, ECO:0000269|PubMed:16893176, ECO:0000269|PubMed:19246009, ECO:0000269|PubMed:8419339, ECO:0000269|PubMed:8494894}.
• Pathway: Terpenoid backbone biosynthesis - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;TGF_beta_Receptor;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: 0.104

Intolerance Scores

• loftool: 0.0803
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.470
• hipred: N
• hipred_score: 0.293
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.872

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fnta
• 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)

Gene ontology

• Biological process: transforming growth factor beta receptor signaling pathway;protein farnesylation;protein geranylgeranylation;neurotransmitter receptor metabolic process;skeletal muscle acetylcholine-gated channel clustering;positive regulation of tubulin deacetylation;positive regulation of deacetylase activity;regulation of neurotransmitter receptor activity
• Cellular component: cytoplasm;cytosol;microtubule associated complex;plasma membrane;CAAX-protein geranylgeranyltransferase complex;protein farnesyltransferase complex
• Molecular function: protein farnesyltransferase activity;protein geranylgeranyltransferase activity;CAAX-protein geranylgeranyltransferase activity;Rab geranylgeranyltransferase activity;protein binding;microtubule binding;acetylcholine receptor regulator activity;receptor tyrosine kinase binding;alpha-tubulin binding