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.

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.

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			42	2	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	1

Variants in CCDC13

This is a list of pathogenic ClinVar variants found in the CCDC13 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-42709035-T-C		not specified	Uncertain significance (Aug 16, 2021)
3-42709060-G-A		not specified	Uncertain significance (Aug 22, 2023)
3-42709762-C-A		not specified	Uncertain significance (May 26, 2023)
3-42709763-C-T		not specified	Uncertain significance (Mar 01, 2024)
3-42713189-G-C		not specified	Uncertain significance (Mar 14, 2023)
3-42713234-G-T		not specified	Uncertain significance (Jan 26, 2023)
3-42713309-C-T		not specified	Uncertain significance (Feb 12, 2024)
3-42730468-G-A		not specified	Uncertain significance (Nov 21, 2022)
3-42730492-C-T		not specified	Uncertain significance (Oct 05, 2021)
3-42730500-C-T		not specified	Uncertain significance (Apr 28, 2023)
3-42730501-G-A		not specified	Uncertain significance (Sep 22, 2023)
3-42730584-G-A		not specified	Likely benign (Oct 03, 2023)
3-42732921-G-A		not specified	Uncertain significance (Jan 22, 2024)
3-42732926-G-A		not specified	Uncertain significance (Dec 03, 2021)
3-42732951-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-42733548-G-A		not specified	Uncertain significance (Dec 06, 2023)
3-42733569-C-A		not specified	Uncertain significance (Dec 16, 2023)
3-42733569-C-T		not specified	Uncertain significance (Jul 26, 2023)
3-42733572-C-A		not specified	Uncertain significance (May 18, 2022)
3-42733576-T-C		not specified	Uncertain significance (Dec 02, 2022)
3-42733603-G-A		not specified	Uncertain significance (Apr 07, 2023)
3-42735772-T-C		not specified	Uncertain significance (Apr 20, 2024)
3-42735805-G-A		not specified	Uncertain significance (Nov 17, 2023)
3-42739639-G-C		not specified	Uncertain significance (Dec 02, 2022)
3-42739729-T-G		not specified	Uncertain significance (Feb 16, 2023)

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