CCDC120

coiled-coil domain containing 120

Basic information

Region (hg38): X:49053572-49069857

Links

ENSG00000147144 ∙ NCBI:90060 ∙ OMIM:300947 ∙ HGNC:28910 ∙ Uniprot:Q96HB5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• osteopetrosis (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC120 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC120 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				2		2
missense			54	4		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	54	6	0

Variants in CCDC120

This is a list of pathogenic ClinVar variants found in the CCDC120 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-49062289-G-A		not specified	Uncertain significance (Dec 15, 2024)
X-49062296-T-G		not specified	Uncertain significance (Feb 22, 2025)
X-49062515-C-T		not specified	Uncertain significance (Mar 20, 2024)
X-49063924-C-T		not specified	Uncertain significance (Mar 26, 2024)
X-49063927-C-T		not specified	Uncertain significance (Oct 18, 2021)
X-49063946-G-A		not specified	Uncertain significance (Jan 14, 2025)
X-49063960-C-G		not specified	Uncertain significance (Mar 07, 2025)
X-49063961-C-T		not specified	Uncertain significance (Feb 06, 2023)
X-49064406-G-A		not specified	Uncertain significance (Jun 28, 2023)
X-49064421-G-A		not specified	Uncertain significance (Dec 08, 2023)
X-49064437-G-A		not specified	Uncertain significance (Oct 01, 2024)
X-49064452-C-T		not specified	Uncertain significance (Dec 28, 2022)
X-49064479-G-A		not specified	Uncertain significance (Dec 02, 2024)
X-49064481-C-T		not specified	Uncertain significance (Oct 04, 2024)
X-49064509-G-C		not specified	Uncertain significance (Aug 11, 2022)
X-49064543-T-C			Likely benign (Jul 01, 2022)
X-49064547-C-T		not specified	Uncertain significance (Jul 14, 2021)
X-49064571-C-T		not specified	Uncertain significance (Apr 04, 2023)
X-49064575-C-T		not specified	Uncertain significance (Dec 15, 2022)
X-49064602-C-T		not specified	Uncertain significance (Jul 15, 2021)
X-49064641-T-C		not specified	Likely benign (Oct 14, 2021)
X-49064649-G-A		not specified	Likely benign (Jul 09, 2024)
X-49065486-C-T		not specified	Uncertain significance (Mar 29, 2022)
X-49065487-G-A		not specified	Uncertain significance (Sep 27, 2024)
X-49065519-C-T		not specified	Uncertain significance (Jan 09, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC120	protein_coding	protein_coding	ENST00000422185	9	16409

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.434	0.565	125202	1	4	125207	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0745	277	281	0.987	0.0000268	4053
Missense in Polyphen		123	127.09	0.96784		1786
Synonymous	-0.209	118	115	1.02	0.00000981	1551
Loss of Function	2.74	3	14.1	0.213	0.00000102	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000367	0.0000367
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000541	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Centriolar protein required for centriole subdistal appendage assembly and microtubule anchoring in interphase cells (PubMed:28422092). Together with CCDC68, cooperate with subdistal appendage components ODF2, NIN and CEP170 for hierarchical subdistal appendage assembly (PubMed:28422092). Recruits NIN and CEP170 to centrosomes (PubMed:28422092). Also required for neurite growth. Localizes CYTH2 to vesicles to allow its transport along neurites, and subsequent ARF6 activation and neurite growth. {ECO:0000269|PubMed:25326380}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.0363
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.208
• hipred: N
• hipred_score: 0.423
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc120
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: multicellular organism development;protein localization;microtubule anchoring at centrosome
• Cellular component: endosome;centriole;growth cone;centriolar subdistal appendage
• Molecular function: protein binding