CCDC61

coiled-coil domain containing 61

Basic information

Region (hg38): 19:45995461-46021318

Links

ENSG00000104983 ∙ NCBI:729440 ∙ ∙ HGNC:33629 ∙ Uniprot:Q9Y6R9 ∙ 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 CCDC61 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC61 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				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in CCDC61

This is a list of pathogenic ClinVar variants found in the CCDC61 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-46016077-C-T			Likely benign (Nov 27, 2017)
19-46019249-G-A		not specified	Uncertain significance (Dec 21, 2022)
19-46019317-C-T		not specified	Uncertain significance (Oct 10, 2023)
19-46019589-C-T		not specified	Uncertain significance (Feb 08, 2023)
19-46019609-C-T		not specified	Uncertain significance (Dec 13, 2022)
19-46019610-G-A		not specified	Uncertain significance (Mar 29, 2022)
19-46019616-C-T		not specified	Uncertain significance (Sep 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC61	protein_coding	protein_coding	ENST00000595358	13	26238

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.26e-14	0.0170	124614	0	42	124656	0.000168

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.607	227	254	0.893	0.0000154	3176
Missense in Polyphen		92	107.72	0.85403		1197
Synonymous	1.25	89	105	0.845	0.00000606	1103
Loss of Function	0.00498	21	21.0	0.999	9.03e-7	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000506	0.000475
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000222
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.000197	0.000195
Middle Eastern	0.000224	0.000222
South Asian	0.000133	0.000131
Other	0.000337	0.000330

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.21

Haploinsufficiency Scores

• pHI: 0.0834
• hipred: N
• hipred_score: 0.275
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.388

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc61

Gene ontology

• Cellular component: centrosome