CCDC22 (CCC complex scaffolding subunit CCDC22)

Gene

• Entrez ID: 28952
• Gene name: CCC complex scaffolding subunit CCDC22
• Gene symbol: CCDC22
• Synonyms (NCBI Gene): CXorf37, JM1, RTSC2
• Chromosome: X
• Chromosome location: Xp11.23
• Summary: This gene encodes a protein containing a coiled-coil domain. The encoded protein functions in the regulation of NF-kB (nuclear factor kappa-light-chain-enhancer of activated B cells) by interacting with COMMD (copper metabolism Murr1 domain-containing) pr

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs140735182	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs143790434	C>A,T	Conflicting-interpretations-of-pathogenicity, benign-likely-benign	Coding sequence variant, non coding transcript variant, missense variant
rs147222955	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, non coding transcript variant, coding sequence variant
rs199809018	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Non coding transcript variant, coding sequence variant, missense variant
rs863225428	A>G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs863225429	A>G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT023813	hsa-miR-1-3p	Proteomics;Microarray	18668037
MIRT040693	hsa-miR-92b-3p	CLASH	23622248
MIRT038882	hsa-miR-93-3p	CLASH	23622248
MIRT868652	hsa-miR-1207-5p	CLIP-seq
MIRT868653	hsa-miR-1909	CLIP-seq
MIRT868654	hsa-miR-4697-3p	CLIP-seq
MIRT868655	hsa-miR-4763-3p	CLIP-seq
MIRT1957762	hsa-miR-214	CLIP-seq
MIRT1957763	hsa-miR-3619-5p	CLIP-seq
MIRT1957764	hsa-miR-4459	CLIP-seq
MIRT1957765	hsa-miR-4722-5p	CLIP-seq
MIRT1957766	hsa-miR-761	CLIP-seq
MIRT2194808	hsa-miR-1184	CLIP-seq
MIRT2194809	hsa-miR-4418	CLIP-seq
MIRT2194810	hsa-miR-509-3-5p	CLIP-seq
MIRT2194811	hsa-miR-509-5p	CLIP-seq
MIRT868652	hsa-miR-1207-5p	CLIP-seq
MIRT868653	hsa-miR-1909	CLIP-seq
MIRT2498109	hsa-miR-296-3p	CLIP-seq
MIRT868654	hsa-miR-4697-3p	CLIP-seq
MIRT868655	hsa-miR-4763-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	23563313, 25355947, 25416956, 26496610, 28514442, 28892079, 29778605, 30833792, 32296183, 32838362, 33060197, 33961781, 34232536, 35271311, 37172566
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IEA
GO:0005813	Component	Centrosome	IDA	26638075
GO:0005813	Component	Centrosome	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0006878	Process	Intracellular copper ion homeostasis	IMP	25355947
GO:0006893	Process	Golgi to plasma membrane transport	IMP	25355947
GO:0015031	Process	Protein transport	IEA
GO:0032456	Process	Endocytic recycling	IMP	28892079
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IMP	23563313
GO:0043124	Process	Negative regulation of canonical NF-kappaB signal transduction	IMP	23563313
GO:0097602	Function	Cullin family protein binding	IBA
GO:0097602	Function	Cullin family protein binding	IDA	23563313
GO:2000060	Process	Positive regulation of ubiquitin-dependent protein catabolic process	IBA
GO:2000060	Process	Positive regulation of ubiquitin-dependent protein catabolic process	IMP	23563313

Other IDs

• MIM: 300859
• HGNC: 28909
• e!Ensembl: ENSG00000101997

Protein

• UniProt ID: O60826
• Protein name: Coiled-coil domain-containing protein 22
• Protein function: Component of the commander complex that is essential for endosomal recycling of transmembrane cargos; the Commander complex is composed of composed of the CCC subcomplex and the retriever subcomplex (PubMed:37172566, PubMed:38459129). Component
• PDB: 8F2U, 8P0V, 8P0W, 8P0X
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05667	DUF812	1 → 597	Protein of unknown function (DUF812)	Family

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed in adult tissues and in fetal liver and brain, with highest levels in prostate and lowest in skeletal muscle. {ECO:0000269|PubMed:21826058}.
• Sequence:

  MEEADRILIHSLRQAGTAVPPDVQTLRAFTTELVVEAVVRCLRVINPAVGSGLSPLLPLA
  MSARFRLAMSLAQACMDLGYPLELGYQNFLYPSEPDLRDLLLFLAERLPTDASEDADQPA
  GDSAILLRAIGSQIRDQLALPWVPPHLRTPKLQHLQGSALQKPFHASRLVVPELSSRGEP
  REFQASPLLLPVPTQVPQPVGRVASLLEHHALQLCQQTGRDRPGDEDWVHRTSRLPPQED
  TRAQRQRLQKQLTEHLRQSWGLLGAPIQARDLGELLQAWGAGAKTGAPKGSRFTHSEKFT
  FHLEPQAQATQVSDVPATSRRPEQVTWAAQEQELESLREQLEGVNRSIEEVEADMKTLGV
  SFVQAESECRHSKLSTAEREQALRLKSRAVELLPDGTANLAKLQLVVENSAQRVIHLAGQ
  WEKHRVPLLAEYRHLRKLQDCRELESSRRLAEIQELHQSVRAAAEEARRKEEVYKQLMSE
  LETLPRDVSRLAYTQRILEIVGNIRKQKEEITKILSDTKELQKEINSLSGKLDRTFAVTD
  ELVFKDAKKDDAVRKAYKYLAALHENCSQLIQTIEDTGTIMREVRDLEEQIETELGKKTL
  SNLEKIREDYRALRQENAGLLGRVREA

• Sequence length: 627

Pathways

Reactome:

Neddylation

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Ritscher-Schinzel syndrome 1	Pathogenic	rs863225428, rs863225429	RCV001028073 RCV001028072	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ritscher-Schinzel syndrome 2	Pathogenic	rs863225428, rs863225429	RCV000202354 RCV000202351	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CCDC22-related disorder	Uncertain significance; Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY	—	Disgenet, GenCC Disgenet, GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial thoracic aortic aneurysm and aortic dissection	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSULIN-DEPENDENT DIABETES MELLITUS SECRETORY DIARRHEA SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RITSCHER-SCHINZEL SYNDROME	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
3C syndrome	3C syndrome	BEFREE	24916641		★☆☆☆☆ Found in Text Mining only
3C syndrome	3C syndrome	ORPHANET_DG	24916641		★☆☆☆☆ Found in Text Mining only
3C syndrome	3C syndrome	Orphanet			★☆☆☆☆ Found in Text Mining only
3C syndrome	3C syndrome	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Anus, Imperforate	Imperforate anus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Aortic Valve Stenosis	Aortic Valve Sclerosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Atrial Septal Defects	Atrial Septal Defect	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	27888057		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	27888057	Associate	★☆☆☆☆ Found in Text Mining only
Brachydactyly	Brachydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Coloboma of the Retina	Retinal coloboma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Camptodactyly	Congenital Camptodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital malrotation of intestine	Congenital malrotation of intestine	HPO_DG			★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn disease	Pubtator	30710380	Associate	★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dandy-Walker Syndrome	Dandy-Walker Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	27888057	Associate	★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Diabetic neuropathy	Pubtator	36717877	Associate	★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ectopic anus	Ectopic anus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Eichsfeld type congenital muscular dystrophy	Eichsfeld type congenital muscular dystrophy	BEFREE	24916641		★☆☆☆☆ Found in Text Mining only
Endometriosis	Endometriosis	BEFREE	28470452		★☆☆☆☆ Found in Text Mining only
Endometriosis	Endometriosis	Pubtator	28470452	Associate	★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG			★☆☆☆☆ Found in Text Mining only
Fundus coloboma	Fundus Coloboma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydronephrosis	Hydronephrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplastic Left Heart Syndrome	Hypoplastic Left Heart Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypospadias	Hypospadias	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	23563313, 23871722, 24916641	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	BEFREE	24916641		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leukemia, Large Granular Lymphocytic	Lymphoblastic Leukemia	BEFREE	30706328		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	27888057, 35767890	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	27888057		★☆☆☆☆ Found in Text Mining only
Lymphohistiocytosis, Hemophagocytic	Lymphohistiocytosis	BEFREE	30706328		★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development, Group II	Malformation of cortical development	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple sclerosis	Pubtator	27888057	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30706328		★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Papilloma	Papilloma	Pubtator	35322929	Associate	★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	Pubtator	27888057	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary Stenosis	Pulmonary Stenosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
RITSCHER-SCHINZEL SYNDROME 2	RITSCHER-SCHINZEL SYNDROME	UNIPROT_DG	21826058, 23563313, 24916641		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RITSCHER-SCHINZEL SYNDROME 2	RITSCHER-SCHINZEL SYNDROME	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Russell-Silver syndrome	Russell-Silver Syndrome	BEFREE	24916641		★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Speech Disorders	Speech Disorders	HPO_DG			★☆☆☆☆ Found in Text Mining only
Syndactyly	Syndactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Syndactyly of fingers	Syndactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Tetralogy of Fallot	Tetralogy of Fallot	HPO_DG			★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	35322929	Associate	★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★☆☆☆☆ Found in Text Mining only
Vitiligo	Vitiligo	Pubtator	27888057	Associate	★☆☆☆☆ Found in Text Mining only