CCDC89

coiled-coil domain containing 89

Basic information

Region (hg38): 11:85683848-85686195

Links

ENSG00000179071 ∙ NCBI:220388 ∙ ∙ HGNC:26762 ∙ Uniprot:Q8N998 ∙ 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 CCDC89 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC89 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in CCDC89

This is a list of pathogenic ClinVar variants found in the CCDC89 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-85685026-G-A		not specified	Uncertain significance (Dec 06, 2022)
11-85685028-T-C		not specified	Uncertain significance (May 17, 2023)
11-85685088-G-T		not specified	Uncertain significance (Jul 30, 2024)
11-85685130-A-G		not specified	Uncertain significance (Dec 17, 2023)
11-85685190-A-C		not specified	Uncertain significance (Oct 16, 2024)
11-85685193-C-T		not specified	Uncertain significance (May 17, 2023)
11-85685199-A-G		not specified	Uncertain significance (Oct 29, 2024)
11-85685230-C-T		not specified	Uncertain significance (Jun 16, 2023)
11-85685277-A-T		not specified	Uncertain significance (Feb 17, 2024)
11-85685278-C-T		not specified	Uncertain significance (Aug 17, 2021)
11-85685302-G-C		not specified	Uncertain significance (Jun 10, 2024)
11-85685314-C-T		not specified	Uncertain significance (Aug 02, 2022)
11-85685373-G-T		not specified	Uncertain significance (Aug 08, 2023)
11-85685393-C-G		not specified	Uncertain significance (Oct 26, 2022)
11-85685507-C-A		not specified	Uncertain significance (Apr 20, 2024)
11-85685529-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-85685583-C-T		not specified	Uncertain significance (Sep 14, 2022)
11-85685587-G-A		not specified	Uncertain significance (Oct 21, 2024)
11-85685614-C-G		not specified	Uncertain significance (Feb 15, 2023)
11-85685641-G-T		not specified	Uncertain significance (Oct 06, 2022)
11-85685655-A-T		not specified	Uncertain significance (Oct 06, 2022)
11-85685668-C-T		not specified	Uncertain significance (Feb 13, 2025)
11-85685722-G-A		not specified	Uncertain significance (Dec 06, 2024)
11-85685730-T-C		not specified	Uncertain significance (Feb 13, 2025)
11-85685790-G-A		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC89	protein_coding	protein_coding	ENST00000316398	1	2428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000785	0.774	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0561	207	209	0.989	0.0000124	2473
Missense in Polyphen		72	72.459	0.99367		802
Synonymous	-1.55	106	87.6	1.21	0.00000495	700
Loss of Function	1.12	8	12.2	0.654	5.27e-7	162

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0835

Intolerance Scores

• loftool: 0.234
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.332
• hipred: N
• hipred_score: 0.144
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.113

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc89

Gene ontology

• Cellular component: nucleus;cytoplasm