CCDC124

coiled-coil domain containing 124

Basic information

Region (hg38): 19:17933015-17943991

Links

ENSG00000007080 ∙ NCBI:115098 ∙ ∙ HGNC:25171 ∙ Uniprot:Q96CT7 ∙ 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 CCDC124 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC124 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in CCDC124

This is a list of pathogenic ClinVar variants found in the CCDC124 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17936443-A-G		not specified	Uncertain significance (Jul 12, 2022)
19-17936496-G-A		not specified	Uncertain significance (Mar 17, 2023)
19-17936509-A-C		not specified	Uncertain significance (Jun 22, 2023)
19-17936515-A-G		not specified	Uncertain significance (Dec 11, 2023)
19-17936544-G-A		not specified	Uncertain significance (Dec 09, 2023)
19-17942742-G-T		not specified	Uncertain significance (Nov 27, 2024)
19-17942752-G-A		not specified	Uncertain significance (Jan 17, 2024)
19-17942785-C-T		not specified	Uncertain significance (Feb 07, 2023)
19-17942789-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-17942822-A-G		not specified	Uncertain significance (Nov 09, 2021)
19-17942839-G-T		not specified	Uncertain significance (Aug 01, 2024)
19-17943263-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-17943291-C-T		not specified	Uncertain significance (Dec 13, 2021)
19-17943332-A-G		not specified	Uncertain significance (Oct 08, 2024)
19-17943333-G-T		not specified	Uncertain significance (Nov 17, 2023)
19-17943519-A-C		not specified	Uncertain significance (Dec 10, 2024)
19-17943522-C-T		not specified	Uncertain significance (Aug 05, 2024)
19-17943590-C-G		not specified	Uncertain significance (May 27, 2022)
19-17943613-C-A		not specified	Uncertain significance (Sep 01, 2021)
19-17943613-C-G		not specified	Uncertain significance (Jul 25, 2023)
19-17943663-C-T		not specified	Uncertain significance (Sep 30, 2024)
19-17943692-G-A		not specified	Uncertain significance (Jun 22, 2021)
19-17943702-A-G		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC124	protein_coding	protein_coding	ENST00000597436	4	10976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.276	0.703	125080	0	6	125086	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.762	133	160	0.831	0.0000125	1435
Missense in Polyphen		36	54.674	0.65845		497
Synonymous	1.13	55	66.7	0.825	0.00000518	431
Loss of Function	1.94	2	7.87	0.254	3.97e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000181	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000359	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for proper progression of late cytokinetic stages. {ECO:0000269|PubMed:23894443}.

Intolerance Scores

• loftool: 0.603
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.236
• hipred: N
• hipred_score: 0.328
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.815

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc124
• Phenotype: liver/biliary system phenotype; respiratory system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: cell cycle;cell division
• Cellular component: microtubule organizing center;cytosol;plasma membrane;midbody
• Molecular function: RNA binding