MARF1
protein-codingmeiosis regulator and mRNA stability factor 1, the group of MicroRNA protein coding host genes|Protein phosphatase 1 regulatory subunits
Gene summary
This gene encodes a putative peroxisomal protein that appears to be conserved across Euteleostomi. In humans, it may be autoantigenic. [provided by RefSeq, Jul 2010]
- KIAA0430
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~48.8 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 MARF1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014647.4. 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 | 3 | 3 | 1 | 7 | ||
| missense | 230 | 14 | 244 | |||
| nonsense | 4 | 4 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 243 | 17 | 1 | 261 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055462.2 | 26 | MANE Select | |
| Ensembl | ENSP00000379654.3 | 26 | MANE Select | |
| RefSeq | NP_001171927.1 | 26 | Standard | |
| RefSeq | NP_001171928.1 | 26 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- double-strand break repair
- female meiotic nuclear division
- regulation of gene expression
- negative regulation of phosphatase activity
- oogenesis
Molecular Function
- molecular_function
- RNA binding
Cellular Component
- peroxisome
- Golgi apparatus
- membrane
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000396368
- Coding exons
- 26
- Length
- 48781
- Individuals with no LoFs
- 124780
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 124795
- p
- 0.0000601
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.73 | 733 | 973 | 0.754 | 0.0000559 | 11445 |
| Missense (PolyPhen) | 228 | 377.79 | 0.60351 | 4582 | ||
| Synonymous | -1.59 | 434 | 394 | 1.10 | 0.0000250 | 3432 |
| Loss of Function | 7.64 | 4 | 75.7 | 0.0528 | 0.00000366 | 957 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential regulator of oogenesis required for female meiotic progression to repress transposable elements and preventing their mobilization, which is essential for the germline integrity. Probably acts via some RNA metabolic process, equivalent to the piRNA system in males, which mediates the repression of transposable elements during meiosis by forming complexes composed of RNAs and governs the methylation and subsequent repression of transposons. Also required to protect from DNA double-strand breaks (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- RVIS EVS
- -1.52
- RVIS percentile EVS
- 3.45
Essentials
- Essential (gene trap)
- H