SPINDOC
protein-codingspindlin interactor and repressor of chromatin binding
Gene summary
Involved in DNA damage response and negative regulation of DNA-templated transcription. Is active in nucleus and site of DNA damage. [provided by Alliance of Genome Resources, Jul 2025]
- C11orf84
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.3 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 SPINDOC variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138471.3. 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 | 2 | 5 | |||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 18 | 2 | 0 | 20 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_612480.1 | 6 | MANE Select | |
| Ensembl | ENSP00000294244.3 | 6 | MANE Select | |
| Ensembl | ENSP00000443715.1 | 2 | Standard | |
| Ensembl | ENSP00000445256.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of transcription, DNA-templated
Molecular Function
- protein binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000294244
- Coding exons
- 6
- Length
- 14331
- Individuals with no LoFs
- 125687
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125693
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.670 | 204 | 233 | 0.876 | 0.0000148 | 2439 |
| Missense (PolyPhen) | 52 | 81.033 | 0.64171 | 860 | ||
| Synonymous | -0.568 | 107 | 99.8 | 1.07 | 0.00000712 | 794 |
| Loss of Function | 3.50 | 0 | 14.3 | 0.00 | 6.96e-7 | 163 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Negatively regulates the transcriptional activator activity of SPIN1 via inhibition of its histone methyl-binding ability. Represses the expression of a number of SPIN1-regulated genes and the SPIN1-mediated activation of the Wnt signaling pathway. Can also inhibit the histone methyl-binding abilities of SPIN2A, SPIN2B, SPIN3 and SPIN4 (PubMed:29061846). {ECO:0000269|PubMed:29061846}.;
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.45
Essentials
- Essential (gene trap)
- N