CCDC24

coiled-coil domain containing 24

Basic information

Region (hg38): 1:43991359-43996528

Links

ENSG00000159214 ∙ NCBI:149473 ∙ ∙ HGNC:28688 ∙ Uniprot:Q8N4L8 ∙ 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 CCDC24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC24 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		1
missense			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	4	0

Variants in CCDC24

This is a list of pathogenic ClinVar variants found in the CCDC24 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-43991892-C-G		not specified	Uncertain significance (Dec 02, 2022)
1-43991921-C-G		not specified	Uncertain significance (May 04, 2022)
1-43991966-G-C		not specified	Uncertain significance (Sep 01, 2021)
1-43992240-A-G		not specified	Uncertain significance (Mar 16, 2022)
1-43992246-G-C		not specified	Uncertain significance (Oct 13, 2023)
1-43992330-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-43992338-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-43992367-C-G		not specified	Likely benign (Mar 27, 2023)
1-43992375-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-43992376-C-T			Likely benign (Feb 01, 2023)
1-43992525-A-G		not specified	Uncertain significance (Apr 06, 2022)
1-43992614-T-C		not specified	Uncertain significance (Jul 14, 2021)
1-43992619-G-T		not specified	Uncertain significance (Mar 31, 2023)
1-43993907-G-T		not specified	Uncertain significance (Feb 03, 2022)
1-43993930-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-43993948-G-T		not specified	Uncertain significance (Nov 07, 2023)
1-43995611-A-G		not specified	Uncertain significance (Dec 01, 2022)
1-43995979-C-T		not specified	Likely benign (Feb 27, 2023)
1-43996054-G-A		not specified	Likely benign (Sep 29, 2023)
1-43996116-G-T		not specified	Uncertain significance (Mar 01, 2024)
1-43996126-C-T		not specified	Uncertain significance (Jul 14, 2023)
1-43996149-G-A		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC24	protein_coding	protein_coding	ENST00000372318	8	5170

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.39e-8	0.215	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.678	198	173	1.15	0.00000896	1941
Missense in Polyphen		61	63.011	0.96808		753
Synonymous	0.340	65	68.6	0.948	0.00000346	645
Loss of Function	0.322	12	13.3	0.904	5.66e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000764	0.000764
Ashkenazi Jewish	0.00	0.00
East Asian	0.000979	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.000979	0.000979
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0858

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.38

Haploinsufficiency Scores

• pHI: 0.0624
• hipred: N
• hipred_score: 0.123
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc24

Gene ontology

• Biological process: blastocyst hatching
• Molecular function: protein binding