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.

not_specified (34 variants)

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. These statistics are base on transcript: NM_001136203.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			34 clinvar			34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	0	0

Loading clinvar variants...

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