CCDC103

coiled-coil domain containing 103, the group of Axonemal dynein assembly factors

Basic information

Region (hg38): 17:44899141-44905390

Links

ENSG00000167131 ∙ NCBI:388389 ∙ OMIM:614677 ∙ HGNC:32700 ∙ Uniprot:Q8IW40 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia 17 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 17 (Moderate), mode of inheritance: AR
• primary ciliary dyskinesia 17 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• primary ciliary dyskinesia 17 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 17	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Pulmonary	Pulmonary and audiologic surveillance may be beneficial to assess respiratory and hearing function and institute early management measures; In order to facilitate mucus clearance, aggressive interventions (eg, chest percussion and oscillatory vest), as well as vaccinations and early and aggressive treatment of respiratory infections may be beneficial, though measures including lobectomy or lung transplantation may be necessary; The condition can involve multiple anomalies, and individuals may require surgery or other interventions related to findings such as congenital cardiac malformations	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Pulmonary	19720631; 20301301; 22581229

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC103 gene.

• Primary ciliary dyskinesia (106 variants)
• Primary ciliary dyskinesia 17 (38 variants)
• not provided (15 variants)
• not specified (5 variants)
• CCDC103-related condition (1 variants)
• Absent inner and outer dynein arms;Primary ciliary dyskinesia;Situs inversus (1 variants)
• Inborn genetic diseases (1 variants)
• Infertility disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC103 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			1	30		31
missense			48	1		49
nonsense	7					7
start loss						0
frameshift	1	3				4
inframe indel			1			1
splice donor/acceptor (+/-2bp)	3					3
splice region			4	2		6
non coding			18	6	6	30
Total	11	3	68	37	6

Highest pathogenic variant AF is 0.0000263

Variants in CCDC103

This is a list of pathogenic ClinVar variants found in the CCDC103 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44899705-T-G		Primary ciliary dyskinesia	Likely benign (Jun 14, 2016)
17-44899719-A-G		Primary ciliary dyskinesia 17	Uncertain significance (Jan 13, 2018)
17-44899728-C-T		Primary ciliary dyskinesia 17	Uncertain significance (Jan 13, 2018)
17-44899734-C-T		Primary ciliary dyskinesia 17	Uncertain significance (Jan 12, 2018)
17-44899738-C-A		Primary ciliary dyskinesia 17	Uncertain significance (Jan 12, 2018)
17-44899756-G-A		Primary ciliary dyskinesia 17	Uncertain significance (Jan 12, 2018)
17-44899795-G-C		Primary ciliary dyskinesia 17	Uncertain significance (Jan 13, 2018)
17-44899824-G-A		Primary ciliary dyskinesia 17	Benign (Jan 13, 2018)
17-44899853-C-T		Primary ciliary dyskinesia 17	Uncertain significance (Jan 13, 2018)
17-44899858-G-A		Primary ciliary dyskinesia 17	Uncertain significance (Jan 13, 2018)
17-44900676-C-A			Benign (Jul 09, 2018)
17-44901003-A-G		Primary ciliary dyskinesia	Uncertain significance (Aug 24, 2021)
17-44901006-G-A		Primary ciliary dyskinesia 17	Uncertain significance (Jan 13, 2018)
17-44901012-ACAT-A		Primary ciliary dyskinesia	Uncertain significance (Oct 30, 2017)
17-44901029-G-C		Primary ciliary dyskinesia • Primary ciliary dyskinesia 17	Conflicting classifications of pathogenicity (Aug 21, 2022)
17-44901046-G-A		Primary ciliary dyskinesia	Likely benign (Oct 30, 2023)
17-44901050-G-A		Primary ciliary dyskinesia	Uncertain significance (Dec 12, 2023)
17-44901057-T-C		Primary ciliary dyskinesia	Uncertain significance (Oct 05, 2021)
17-44901059-A-G		Primary ciliary dyskinesia	Likely benign (Nov 17, 2023)
17-44901064-T-A		Primary ciliary dyskinesia	Likely benign (Jul 19, 2023)
17-44901064-T-C		Primary ciliary dyskinesia	Likely benign (Nov 14, 2023)
17-44901067-T-C		Primary ciliary dyskinesia	Likely benign (Apr 28, 2023)
17-44901070-G-A		Primary ciliary dyskinesia 17 • Primary ciliary dyskinesia	Conflicting classifications of pathogenicity (Dec 26, 2023)
17-44901076-C-T		Primary ciliary dyskinesia	Likely benign (Mar 22, 2023)
17-44901079-A-G		Primary ciliary dyskinesia	Likely benign (Apr 20, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC103	protein_coding	protein_coding	ENST00000417826	3	6249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000509	0.703	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0869	133	136	0.979	0.00000802	1547
Missense in Polyphen		36	44.03	0.81762		518
Synonymous	-0.0436	57	56.6	1.01	0.00000317	510
Loss of Function	0.842	6	8.68	0.692	5.52e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000605	0.000600
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dynein-attachment factor required for cilia motility. {ECO:0000269|PubMed:22581229}.
• Disease: DISEASE: Ciliary dyskinesia, primary, 17 (CILD17) [MIM:614679]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269|PubMed:22581229, ECO:0000269|PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.562
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.197
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc103

Zebrafish Information Network

• Gene name: ccdc103
• Affected structure: ciliated olfactory receptor neuron
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Biological process: heart looping;cilium movement;outer dynein arm assembly;inner dynein arm assembly;epithelial cilium movement involved in determination of left/right asymmetry;axonemal dynein complex assembly;determination of digestive tract left/right asymmetry
• Cellular component: cytoplasm;axoneme;motile cilium
• Molecular function: protein binding;protein homodimerization activity