CEP112
protein-codingcentrosomal protein 112
Gene summary
This gene encodes a coiled-coil domain containing protein that belongs to the cell division control protein 42 effector protein family. In neurons, it localizes to the cytoplasm of dendrites and is also enriched in the nucleus where it interacts with the RNA polymerase III transcriptional repressor Maf1 to regulate gamma-aminobutyric acid A receptor surface expression. In addition, the protein has been identified as a component of the human centrosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
- CCDC46
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~556.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0033622
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Genitourinary
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CEP112 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001199165.4. 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 | 2 | 1 | 4 | ||
| missense | 1 | 97 | 5 | 103 | ||
| nonsense | 1 | 1 | 2 | |||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 9 | 10 | |||
| Total | 2 | 2 | 108 | 7 | 1 | 120 |
Highest pathogenic variant AF is 0.000032841657
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001186094.1 | 26 | MANE Select | |
| Ensembl | ENSP00000442784.2 | 26 | MANE Select | |
| RefSeq | NP_001032402.1 | 7 | Standard | |
| RefSeq | NP_001289820.1 | 24 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- receptor localization to synapse
Cellular Component
- cytoplasm
- centrosome
- plasma membrane
- inhibitory synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000392769
- Coding exons
- 26
- Length
- 556547
- Individuals with no LoFs
- 125451
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 297
- Defined
- 125748
- p
- 0.00118
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0232 | 478 | 479 | 0.997 | 0.0000254 | 6318 |
| Missense (PolyPhen) | 159 | 178.48 | 0.89086 | 2426 | ||
| Synonymous | 0.151 | 166 | 168 | 0.985 | 0.00000868 | 1610 |
| Loss of Function | 0.668 | 62 | 67.9 | 0.912 | 0.00000377 | 791 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00080 | 0.00080 | rare |
| Latino/Admixed American | 0.00077 | 0.00075 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.0017 | 0.0017 | notable |
| Finnish | 0.0039 | 0.0039 | notable |
| European (Non-Finnish) | 0.00076 | 0.00075 | rare |
| South Asian | 0.0016 | 0.0016 | notable |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- -0.46
- RVIS percentile EVS
- 23.69
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |