CCDC33

coiled-coil domain containing 33, the group of C2 domain containing

Basic information

Region (hg38): 15:74202705-74336472

Links

ENSG00000140481 ∙ NCBI:80125 ∙ OMIM:618525 ∙ HGNC:26552 ∙ Uniprot:Q8N5R6 ∙ 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 CCDC33 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC33 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			48	10		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	10	0

Variants in CCDC33

This is a list of pathogenic ClinVar variants found in the CCDC33 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74202725-C-G		Matthew-Wood syndrome	Uncertain significance (Jan 15, 2018)
15-74202780-C-T		Matthew-Wood syndrome	Uncertain significance (Jan 12, 2018)
15-74202797-C-T		Syndromic Microphthalmia, Recessive	Uncertain significance (Jun 14, 2016)
15-74202810-T-C		Syndromic Microphthalmia, Recessive	Uncertain significance (Jun 14, 2016)
15-74202836-G-T		Syndromic Microphthalmia, Recessive	Uncertain significance (Jun 14, 2016)
15-74203033-A-C			Benign (Aug 14, 2018)
15-74203214-TTG-T			Benign (Jun 19, 2018)
15-74207615-G-C			Benign (Jun 26, 2018)
15-74207639-C-T			Benign (Oct 22, 2019)
15-74207712-C-T			Benign (May 21, 2021)
15-74207720-A-C			Uncertain significance (-)
15-74207736-G-A		STRA6-related disorder	Likely benign (Jul 19, 2021)
15-74207739-G-C			Likely benign (Jun 29, 2018)
15-74207764-G-A			Benign (Jun 19, 2018)
15-74207897-C-T			Benign (Jun 19, 2018)
15-74208006-C-G			Benign (Aug 21, 2019)
15-74208389-C-T			Benign (Jun 26, 2018)
15-74209236-G-A			Likely benign (Dec 09, 2018)
15-74209398-C-T		STRA6-related disorder	Likely benign (Aug 07, 2019)
15-74209420-A-T		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
15-74217353-C-A			Likely benign (May 01, 2023)
15-74244015-G-A		CCDC33-related disorder	Likely benign (Apr 29, 2022)
15-74244033-C-A		not specified	Uncertain significance (May 30, 2023)
15-74244062-G-C		not specified	Likely benign (Dec 28, 2022)
15-74244085-T-G		not specified	Uncertain significance (Apr 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC33	protein_coding	protein_coding	ENST00000398814	19	119201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.96e-20	0.0393	124646	0	167	124813	0.000669

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00592	428	428	1.00	0.0000247	4892
Missense in Polyphen		151	151.87	0.9943		1689
Synonymous	-0.0231	176	176	1.00	0.0000100	1497
Loss of Function	1.05	34	41.3	0.824	0.00000222	459

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00376	0.00376
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000502	0.000445
Finnish	0.000233	0.000232
European (Non-Finnish)	0.000523	0.000521
Middle Eastern	0.000502	0.000445
South Asian	0.000656	0.000654
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0870

Intolerance Scores

• loftool: 0.941
• rvis_EVS: 1.14
• rvis_percentile_EVS: 92.34

Haploinsufficiency Scores

• pHI: 0.0878
• hipred: N
• hipred_score: 0.200
• ghis: 0.420

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc33
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

• Molecular function: protein binding