CCSAP

centriole, cilia and spindle associated protein

Basic information

Region (hg38): 1:229321010-229343294

Previous symbols: [ "C1orf96" ]

Links

ENSG00000154429 ∙ NCBI:126731 ∙ OMIM:616762 ∙ HGNC:29578 ∙ Uniprot:Q6IQ19 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCSAP gene.

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: gnomAD

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: dbNSFP

• 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 Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccsap

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