CCDC80

coiled-coil domain containing 80

Basic information

Region (hg38): 3:112596796-112649530

Previous symbols: [ "LINC01279" ]

Links

ENSG00000091986 ∙ NCBI:151887 ∙ OMIM:608298 ∙ HGNC:30649 ∙ Uniprot:Q76M96 ∙ 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 CCDC80 gene.

• Inborn genetic diseases (42 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC80 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				1	2	3
missense			37	7	2	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	8	4

Variants in CCDC80

This is a list of pathogenic ClinVar variants found in the CCDC80 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-112605424-G-A		not specified	Uncertain significance (Aug 26, 2022)
3-112605458-A-G			Likely benign (Apr 01, 2023)
3-112605527-C-T		not specified	Uncertain significance (Jun 27, 2022)
3-112605679-A-T		not specified	Uncertain significance (Dec 22, 2023)
3-112605688-G-A		not specified	Uncertain significance (Apr 04, 2023)
3-112605719-T-C		not specified	Uncertain significance (Jan 05, 2022)
3-112605737-C-T		not specified	Likely benign (Jun 24, 2022)
3-112605740-C-T		not specified	Uncertain significance (Sep 27, 2022)
3-112607200-C-T		not specified	Uncertain significance (Dec 15, 2022)
3-112607241-G-A		not specified	Uncertain significance (Dec 21, 2022)
3-112609989-G-A			Benign (May 30, 2018)
3-112610076-C-T		not specified	Uncertain significance (Jul 15, 2021)
3-112610077-G-A		not specified	Uncertain significance (Aug 02, 2023)
3-112616720-A-C		not specified	Uncertain significance (Jul 09, 2021)
3-112616819-C-G		not specified	Uncertain significance (Jan 11, 2023)
3-112619034-C-G		not specified	Uncertain significance (Dec 19, 2022)
3-112619053-C-T		not specified	Likely benign (Feb 05, 2024)
3-112619066-A-T		not specified	Uncertain significance (Feb 05, 2024)
3-112630124-T-G		not specified	Uncertain significance (Feb 17, 2024)
3-112630224-G-A		not specified	Uncertain significance (Jul 27, 2021)
3-112638030-G-A		not specified	Uncertain significance (Jan 19, 2022)
3-112638040-T-G		not specified	Uncertain significance (Aug 08, 2022)
3-112638045-C-T		not specified	Uncertain significance (May 30, 2023)
3-112638066-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-112638067-G-C			Likely benign (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC80	protein_coding	protein_coding	ENST00000206423	7	44971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000600	1.00	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.441	522	551	0.947	0.0000330	6214
Missense in Polyphen		186	220.09	0.8451		2588
Synonymous	-0.299	218	212	1.03	0.0000133	1881
Loss of Function	3.19	15	35.5	0.422	0.00000196	433

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000628	0.000628
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000178	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes cell adhesion and matrix assembly. {ECO:0000250}.

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.737
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.28

Haploinsufficiency Scores

• pHI: 0.606
• hipred: Y
• hipred_score: 0.544
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.565

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc80
• Phenotype: digestive/alimentary phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; neoplasm; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: ccdc80
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Biological process: response to bacterium;positive regulation of cell-substrate adhesion;extracellular matrix organization
• Cellular component: basement membrane;interstitial matrix
• Molecular function: fibronectin binding;heparin binding