CCDC13

coiled-coil domain containing 13

Basic information

Region (hg38): 3:42705756-42773253

Links

ENSG00000244607 ∙ NCBI:152206 ∙ ∙ HGNC:26358 ∙ Uniprot:Q8IYE1 ∙ 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 CCDC13 gene.

• not_specified (104 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000144719.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			93	10	1	104
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	11	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC13	protein_coding	protein_coding	ENST00000310232	15	80591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.03e-9	0.999	125333	2	413	125748	0.00165

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.570	387	420	0.922	0.0000252	4628
Missense in Polyphen		114	136.15	0.83732		1460
Synonymous	1.55	149	175	0.851	0.0000107	1414
Loss of Function	2.95	20	40.2	0.497	0.00000230	426

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00117
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.0133	0.0133
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000493	0.000475
Middle Eastern	0.0133	0.0133
South Asian	0.00242	0.00239
Other	0.000978	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for primary cilia formation and promotes the localization of the ciliopathy protein BBS4 to both centriolar satellites and cilia. {ECO:0000269|PubMed:24816561}.

Intolerance Scores

• loftool: 0.924
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.85

Haploinsufficiency Scores

• pHI: 0.0817
• hipred: N
• hipred_score: 0.413
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc13

Gene ontology

• Biological process: cellular response to DNA damage stimulus;cytoplasmic microtubule organization;non-motile cilium assembly
• Cellular component: nucleus;centrosome;cytosol;centriolar satellite;cell projection
• Molecular function: protein binding