CCSAP
Basic information
Region (hg38): 1:229321011-229343294
Previous symbols: [ "C1orf96" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCSAP gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 12 | 12 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 12 | 0 | 0 |
Variants in CCSAP
This is a list of pathogenic ClinVar variants found in the CCSAP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-229325369-C-T | not specified | Uncertain significance (Aug 12, 2022) | ||
1-229326945-G-T | not specified | Uncertain significance (May 09, 2022) | ||
1-229326953-C-G | not specified | Uncertain significance (Sep 27, 2022) | ||
1-229326974-C-T | not specified | Uncertain significance (Nov 27, 2023) | ||
1-229326985-T-C | not specified | Uncertain significance (Dec 22, 2023) | ||
1-229342129-C-T | not specified | Uncertain significance (Sep 30, 2021) | ||
1-229342141-C-G | not specified | Uncertain significance (Aug 30, 2022) | ||
1-229342164-G-A | not specified | Uncertain significance (May 03, 2023) | ||
1-229342254-C-T | not specified | Uncertain significance (May 25, 2022) | ||
1-229342270-A-C | not specified | Uncertain significance (Jul 13, 2021) | ||
1-229342357-G-A | not specified | Uncertain significance (Jan 11, 2023) | ||
1-229342425-C-T | not specified | Uncertain significance (Aug 17, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CCSAP | protein_coding | protein_coding | ENST00000284617 | 3 | 22284 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.105 | 0.867 | 125739 | 0 | 8 | 125747 | 0.0000318 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.46 | 75 | 120 | 0.625 | 0.00000619 | 1704 |
Missense in Polyphen | 20 | 42.272 | 0.47313 | 533 | ||
Synonymous | -0.0193 | 51 | 50.8 | 1.00 | 0.00000306 | 532 |
Loss of Function | 1.88 | 3 | 9.13 | 0.328 | 4.57e-7 | 119 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.000298 | 0.000298 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000265 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in microtubule (MT) stabilization and this stabilization involves the maintenance of NUMA1 at the spindle poles. Colocalizes with polyglutamylated MTs to promote MT stabilization and regulate bipolar spindle formation in mitosis. Binding of CCSAP to centrosomes and the spindle around centrosomes during mitosis inhibits MT depolymerization, thereby stabilizing the mitotic spindle (PubMed:26562023). May play a role in embryonic development. May be required for proper cilia beating (By similarity). {ECO:0000250|UniProtKB:Q6P3G4, ECO:0000269|PubMed:26562023}.;
Haploinsufficiency Scores
- pHI
- 0.223
- hipred
- N
- hipred_score
- 0.378
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccsap
- Phenotype
Zebrafish Information Network
- Gene name
- ccsapb
- Affected structure
- Mauthner neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- cell cycle;multicellular organism development;regulation of embryonic development;cell division;regulation of cilium beat frequency involved in ciliary motility;regulation of mitotic spindle assembly;mitotic spindle microtubule depolymerization
- Cellular component
- centrosome;centriole;spindle;cilium;axoneme;axon;ciliary transition zone;ciliary basal body;mitotic spindle astral microtubule;mitotic spindle
- Molecular function
- microtubule binding