CCDC60

coiled-coil domain containing 60

Basic information

Region (hg38): 12:119334712-119541040

Links

ENSG00000183273 ∙ NCBI:160777 ∙ ∙ HGNC:28610 ∙ Uniprot:Q8IWA6 ∙ 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 CCDC60 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC60 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			36	2		38
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	0

Variants in CCDC60

This is a list of pathogenic ClinVar variants found in the CCDC60 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-119335229-C-T		not specified	Uncertain significance (Jun 13, 2024)
12-119428721-C-G		not specified	Uncertain significance (Sep 13, 2023)
12-119428725-G-C		not specified	Uncertain significance (Jan 26, 2022)
12-119428740-A-G		not specified	Uncertain significance (May 31, 2022)
12-119428762-G-A		not specified	Uncertain significance (Jun 28, 2022)
12-119472001-A-G		not specified	Uncertain significance (Feb 21, 2024)
12-119472110-A-C		not specified	Uncertain significance (Aug 12, 2021)
12-119472154-AC-A			Likely benign (Feb 01, 2024)
12-119479109-G-C		not specified	Uncertain significance (Mar 15, 2024)
12-119479149-T-C		not specified	Uncertain significance (Jan 24, 2023)
12-119479160-C-G		not specified	Uncertain significance (Oct 10, 2023)
12-119488760-G-A		not specified	Uncertain significance (Apr 28, 2022)
12-119488772-C-T		not specified	Uncertain significance (Jun 11, 2021)
12-119488823-A-G		not specified	Uncertain significance (Jul 12, 2022)
12-119488828-C-G		not specified	Uncertain significance (Feb 22, 2023)
12-119500142-T-G		not specified	Uncertain significance (Jan 26, 2022)
12-119505095-G-A		not specified	Uncertain significance (May 26, 2023)
12-119505096-C-G		not specified	Uncertain significance (Jan 30, 2024)
12-119505127-G-T		not specified	Uncertain significance (Jan 19, 2022)
12-119505154-G-T		not specified	Uncertain significance (Sep 28, 2022)
12-119505156-G-C		not specified	Uncertain significance (Jul 12, 2023)
12-119516650-G-A		not specified	Uncertain significance (Mar 03, 2022)
12-119516661-C-T		not specified	Uncertain significance (Mar 29, 2023)
12-119520138-A-G		not specified	Likely benign (Oct 26, 2021)
12-119522967-A-G		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC60	protein_coding	protein_coding	ENST00000327554	14	206336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.71e-10	0.887	125274	1	472	125747	0.00188

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.142	307	314	0.977	0.0000172	3644
Missense in Polyphen		116	118.51	0.97886		1363
Synonymous	1.93	85	111	0.767	0.00000572	1012
Loss of Function	1.80	19	29.5	0.643	0.00000158	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00260	0.00258
Ashkenazi Jewish	0.000797	0.000794
East Asian	0.000598	0.000598
Finnish	0.00255	0.00254
European (Non-Finnish)	0.00200	0.00200
Middle Eastern	0.000598	0.000598
South Asian	0.00302	0.00275
Other	0.00261	0.00261

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0760

Intolerance Scores

• loftool: 0.984
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.82

Haploinsufficiency Scores

• pHI: 0.0796
• hipred: N
• hipred_score: 0.384
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc60

Gene ontology

• Molecular function: protein binding