FNTA
farnesyltransferase, CAAX box, alpha, the group of Prenyltransferase alpha subunit repeat containing
Basic information
Region (hg38): 8:43034194-43085788
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (40 variants)
- not_provided (2 variants)
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. These statistics are base on transcript: NM_000002027.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 40 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 0 | 2 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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