CCDC9

coiled-coil domain containing 9

Basic information

Region (hg38): 19:47255980-47273701

Links

ENSG00000105321 ∙ NCBI:26093 ∙ ∙ HGNC:24560 ∙ Uniprot:Q9Y3X0 ∙ 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 CCDC9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC9 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			72	3		75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	72	5	0

Variants in CCDC9

This is a list of pathogenic ClinVar variants found in the CCDC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47258599-C-T		not specified	Uncertain significance (Feb 02, 2024)
19-47258619-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-47258653-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-47260360-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-47260379-G-A		not specified	Uncertain significance (Jun 17, 2024)
19-47260408-G-A		not specified	Likely benign (Sep 01, 2021)
19-47260408-G-C		not specified	Uncertain significance (May 23, 2023)
19-47260628-C-T		not specified	Uncertain significance (Oct 03, 2022)
19-47260651-G-C		not specified	Uncertain significance (Oct 04, 2024)
19-47260664-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-47260670-A-G		not specified	Uncertain significance (Sep 17, 2021)
19-47260681-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-47260682-G-A		not specified	Uncertain significance (Dec 16, 2024)
19-47260690-A-G		not specified	Uncertain significance (Mar 29, 2023)
19-47260692-G-A		not specified	Uncertain significance (Jan 17, 2024)
19-47260706-G-A		not specified	Uncertain significance (Oct 16, 2023)
19-47260729-G-A		not specified	Uncertain significance (Jun 25, 2024)
19-47260759-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-47260765-C-T		not specified	Uncertain significance (May 14, 2024)
19-47260774-C-T		not specified	Uncertain significance (Feb 13, 2025)
19-47260789-C-T		not specified	Uncertain significance (Oct 07, 2024)
19-47260810-G-A		not specified	Uncertain significance (Feb 12, 2024)
19-47260811-A-G		not specified	Uncertain significance (Feb 12, 2024)
19-47260828-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-47260829-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC9	protein_coding	protein_coding	ENST00000221922	11	15974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000290	0.997	125729	0	16	125745	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.179	344	335	1.03	0.0000227	3361
Missense in Polyphen		118	137	0.8613		1217
Synonymous	-1.42	142	122	1.16	0.00000739	1056
Loss of Function	2.62	12	26.5	0.452	0.00000149	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000630	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000246	0.000231
European (Non-Finnish)	0.0000544	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000991	0.0000980
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.639
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.14

Haploinsufficiency Scores

• pHI: 0.238
• hipred: N
• hipred_score: 0.144
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.372

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc9

Gene ontology

• Molecular function: RNA binding;protein binding