FIGNL1
protein-codingfidgetin like 1, the group of AAA ATPases
Gene summary
This gene encodes a member of the AAA ATPase family of proteins. The encoded protein is recruited to sites of DNA damage where it plays a role in DNA double-strand break repair via homologous recombination. This protein has also been shown to localize to the centrosome and inhibit ciliogenesis, and may regulate the proliferation and differentiation of osteoblasts. [provided by RefSeq, Oct 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to FIGNL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001287492.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 93 | 5 | 98 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 94 | 5 | 1 | 100 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001274421.1 | 1 | MANE Select | |
| Ensembl | ENSP00000399997.1 | 1 | MANE Select | |
| RefSeq | NP_001036227.1 | 1 | Standard | |
| RefSeq | NP_001274422.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- osteoblast differentiation
- male meiotic nuclear division
- regulation of double-strand break repair via homologous recombination
- cytoplasmic microtubule organization
- osteoblast proliferation
Molecular Function
- magnesium ion binding
- protein binding
- ATP binding
- microtubule-severing ATPase activity
- hydrolase activity
Cellular Component
- nuclear chromosome
- nucleus
- cytoplasm
- perinuclear region of cytoplasm
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000419119
- Coding exons
- 1
- Length
- 6258
- Individuals with no LoFs
- 125592
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 155
- Defined
- 125747
- p
- 0.000617
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.522 | 389 | 361 | 1.08 | 0.0000185 | 4420 |
| Missense (PolyPhen) | 99 | 106.48 | 0.92977 | 1242 | ||
| Synonymous | -0.376 | 129 | 124 | 1.04 | 0.00000587 | 1345 |
| Loss of Function | 2.30 | 10 | 21.5 | 0.464 | 0.00000122 | 261 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00023 | 0.00023 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00092 | 0.00091 | rare |
| South Asian | 0.00065 | 0.00065 | rare |
| Other | 0.0011 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in DNA double-strand break (DBS) repair via homologous recombination (HR). Recruited at DSB sites independently of BRCA2, RAD51 and RAD51 paralogs in a H2AX- dependent manner. May regulate osteoblast proliferation and differentiation (PubMed:23754376). May play a role in the control of male meiosis dynamic (By similarity). {ECO:0000250|UniProtKB:Q8BPY9, ECO:0000269|PubMed:23754376}.;
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- LoFtool
- 0.0886
- RVIS EVS
- 0.09
- RVIS percentile EVS
- 60.71
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.125
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |