FDX1
ferredoxin 1, the group of Ferredoxin family
Basic information
Region (hg38): 11:110429948-110464884
Previous symbols: [ "FDX" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FDX1 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 | |||||
| missense | 12 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 2 | 1 |
Variants in FDX1
This is a list of pathogenic ClinVar variants found in the FDX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-110430130-G-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 11-110430133-G-A | not specified | Uncertain significance (Jun 10, 2021) | ||
| 11-110430181-G-C | not specified | Uncertain significance (Dec 16, 2021) | ||
| 11-110430182-C-G | not specified | Uncertain significance (Dec 16, 2021) | ||
| 11-110430182-C-T | not specified | Uncertain significance (Jul 13, 2022) | ||
| 11-110430187-C-T | not specified | Uncertain significance (Jun 03, 2024) | ||
| 11-110430194-T-C | not specified | Uncertain significance (May 14, 2024) | ||
| 11-110430199-C-G | not specified | Uncertain significance (Nov 21, 2023) | ||
| 11-110430242-G-C | not specified | Uncertain significance (Jun 10, 2021) | ||
| 11-110430245-G-A | not specified | Uncertain significance (Jan 09, 2024) | ||
| 11-110435922-G-A | not specified | Uncertain significance (Oct 16, 2023) | ||
| 11-110435944-A-G | not specified | Uncertain significance (Jun 29, 2022) | ||
| 11-110456974-A-G | not specified | Uncertain significance (Apr 08, 2024) | ||
| 11-110456995-A-G | not specified | Uncertain significance (May 27, 2022) | ||
| 11-110457021-C-T | Benign (Dec 31, 2019) | |||
| 11-110462385-A-G | not specified | Uncertain significance (Nov 09, 2021) | ||
| 11-110462445-A-G | not specified | Likely benign (Dec 19, 2023) | ||
| 11-110462451-G-A | not specified | Likely benign (Mar 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FDX1 | protein_coding | protein_coding | ENST00000260270 | 4 | 34999 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0866 | 0.773 | 125721 | 0 | 6 | 125727 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.448 | 57 | 67.4 | 0.846 | 0.00000337 | 1167 |
| Missense in Polyphen | 26 | 34.483 | 0.754 | 397 | ||
| Synonymous | -0.256 | 25 | 23.4 | 1.07 | 0.00000101 | 405 |
| Loss of Function | 1.10 | 2 | 4.51 | 0.443 | 1.87e-7 | 81 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000151 | 0.000149 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential for the synthesis of various steroid hormones (PubMed:20547883, PubMed:21636783). Participates in the reduction of mitochondrial cytochrome P450 for steroidogenesis (PubMed:20547883, PubMed:21636783). Transfers electrons from adrenodoxin reductase to CYP11A1, a cytochrome P450 that catalyzes cholesterol side-chain cleavage (PubMed:20547883, PubMed:21636783). Does not form a ternary complex with adrenodoxin reductase and CYP11A1 but shuttles between the two enzymes to transfer electrons (By similarity). {ECO:0000250|UniProtKB:P00257, ECO:0000269|PubMed:20547883, ECO:0000269|PubMed:21636783}.;
- Pathway
- Phase I - Functionalization of compounds;Electron transport from NADPH to Ferredoxin;Metabolism of lipids;Endogenous sterols;Cytochrome P450 - arranged by substrate type;Biological oxidations;Mitochondrial iron-sulfur cluster biogenesis;Metabolism;folate transformations I;Pregnenolone biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Steroid hormones
(Consensus)
Recessive Scores
- pRec
- 0.307
Haploinsufficiency Scores
- pHI
- 0.182
- hipred
- N
- hipred_score
- 0.206
- ghis
- 0.484
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.823
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fdx1
- Phenotype
- vision/eye 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- fdx1
- Affected structure
- epiboly involved in gastrulation with mouth forming second
- Phenotype tag
- abnormal
- Phenotype quality
- delayed
Gene ontology
- Biological process
- C21-steroid hormone biosynthetic process;cholesterol metabolic process;sterol metabolic process;electron transport chain;hormone biosynthetic process;small molecule metabolic process;cellular response to cAMP;cellular response to forskolin
- Cellular component
- mitochondrion;mitochondrial matrix
- Molecular function
- iron ion binding;electron transfer activity;2 iron, 2 sulfur cluster binding