SPIN2A
protein-codingspindlin family member 2A, the group of Spindlin family|Tudor domain containing
Gene summary
This gene encodes one of three members of the DXF34 gene family, located in a 100-kb region of chromosome Xp11.21. [provided by RefSeq, Nov 2009]
- SPIN2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.0 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 SPIN2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_019003.5. 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 | 38 | 2 | 40 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 38 | 3 | 0 | 41 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061876.3 | 1 | MANE Select | |
| Ensembl | ENSP00000364041.3 | 1 | MANE Select | |
| Ensembl | ENSP00000364043.1 | 1 | Standard | |
| Ensembl | ENSP00000483149.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cell cycle
- gamete generation
- regulation of cell cycle
Molecular Function
- molecular_function
- protein binding
- methylated histone binding
Cellular Component
- cellular_component
- nucleoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000374908
- Coding exons
- 1
- Length
- 3096
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.03 | 100 | 74.8 | 1.34 | 0.00000517 | 1691 |
| Missense (PolyPhen) | 37 | 24.623 | 1.5027 | 558 | ||
| Synonymous | -0.624 | 31 | 26.9 | 1.15 | 0.00000188 | 500 |
| Loss of Function | -0.250 | 4 | 3.50 | 1.14 | 2.46e-7 | 94 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in the regulation of cell cycle progression (By similarity). Exhibits H3K4me3-binding activity (PubMed:29061846). {ECO:0000250|UniProtKB:Q9BPZ2, ECO:0000269|PubMed:29061846}.;
Recessive Scores
- pRec
- 0.121
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0902
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |