ODF1
protein-codingouter dense fiber of sperm tails 1, the group of Small heat shock proteins
Gene summary
The outer dense fibers are cytoskeletal structures that surround the axoneme in the middle piece and principal piece of the sperm tail. The fibers function in maintaining the elastic structure and recoil of the sperm tail as well as in protecting the tail from shear forces during epididymal transport and ejaculation. Defects in the outer dense fibers lead to abnormal sperm morphology and infertility. The human outer dense fibers contains at least 10 major proteins and this gene encodes the main protein. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.4 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 ODF1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024410.4. 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 | 0 | |||||
| missense | 30 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 30 | 0 | 0 | 30 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_077721.2 | 2 | MANE Select | |
| Ensembl | ENSP00000285402.3 | 2 | MANE Select | |
| Ensembl | ENSP00000430023.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- multicellular organism development
- spermatogenesis
- cell differentiation
Molecular Function
- protein binding
- protein domain specific binding
Cellular Component
- outer dense fiber
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000285402
- Coding exons
- 2
- Length
- 9446
- Individuals with no LoFs
- 124825
- Homozygous LoFs
- 15
- Heterozygous LoFs
- 793
- Defined
- 125633
- p
- 0.00322
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.680 | 123 | 146 | 0.842 | 0.00000825 | 1629 |
| Missense (PolyPhen) | 37 | 51.25 | 0.72195 | 562 | ||
| Synonymous | 0.435 | 57 | 61.3 | 0.929 | 0.00000394 | 461 |
| Loss of Function | 3.08 | 0 | 11.0 | 0.00 | 7.79e-7 | 128 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.10 | 0.042 | notable |
| Latino/Admixed American | 0.0067 | 0.0027 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00011 | rare |
| Finnish | 0.00011 | 0.000046 | rare |
| European (Non-Finnish) | 0.00061 | 0.00026 | rare |
| South Asian | 0.00023 | 0.000098 | rare |
| Other | 0.0047 | 0.0021 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the outer dense fibers (ODF) of spermatozoa. ODF are filamentous structures located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail and may help to maintain the passive elastic structures and elastic recoil of the sperm tail.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.435
- RVIS EVS
- 0.6
- RVIS percentile EVS
- 82.66
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.496
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |