CCDC120
protein-codingcoiled-coil domain containing 120
Gene summary
This gene encodes a protein that contains a coiled-coil domain. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Nov 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: XL
Disease ID:MONDO:0017198
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CCDC120 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001163321.4. 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 | 6 | 2 | 8 | |||
| missense | 113 | 5 | 118 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 1 | 6 | |||
| Total | 0 | 0 | 126 | 8 | 0 | 134 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001156793.2 | 10 | MANE Select | |
| Ensembl | ENSP00000474071.1 | 10 | MANE Select | |
| RefSeq | NP_001156794.1 | 9 | Standard | |
| RefSeq | NP_001156795.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- multicellular organism development
- protein localization
- microtubule anchoring at centrosome
Molecular Function
- protein binding
Cellular Component
- endosome
- centriole
- growth cone
- centriolar subdistal appendage
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000422185
- Coding exons
- 9
- Length
- 16409
- Individuals with no LoFs
- 125202
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 4
- Defined
- 125207
- p
- 0.0000200
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0745 | 277 | 281 | 0.987 | 0.0000268 | 4053 |
| Missense (PolyPhen) | 123 | 127.09 | 0.96784 | 1786 | ||
| Synonymous | -0.209 | 118 | 115 | 1.02 | 0.00000981 | 1551 |
| Loss of Function | 2.74 | 3 | 14.1 | 0.213 | 0.00000102 | 256 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000037 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000054 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Centriolar protein required for centriole subdistal appendage assembly and microtubule anchoring in interphase cells (PubMed:28422092). Together with CCDC68, cooperate with subdistal appendage components ODF2, NIN and CEP170 for hierarchical subdistal appendage assembly (PubMed:28422092). Recruits NIN and CEP170 to centrosomes (PubMed:28422092). Also required for neurite growth. Localizes CYTH2 to vesicles to allow its transport along neurites, and subsequent ARF6 activation and neurite growth. {ECO:0000269|PubMed:25326380}.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- LoFtool
- 0.0363
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0645
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |