CCDC88B

coiled-coil domain containing 88B

Basic information

Region (hg38): 11:64340204-64357534

Previous symbols: [ "CCDC88" ]

Links

ENSG00000168071 ∙ NCBI:283234 ∙ OMIM:611205 ∙ HGNC:26757 ∙ Uniprot:A6NC98 ∙ 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 CCDC88B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC88B 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	1	2
missense			114	4		118
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	114	5	1

Variants in CCDC88B

This is a list of pathogenic ClinVar variants found in the CCDC88B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64340273-G-A		not specified	Uncertain significance (Nov 29, 2023)
11-64340672-G-C		not specified	Uncertain significance (Oct 03, 2022)
11-64340679-C-G		not specified	Uncertain significance (Dec 13, 2022)
11-64340718-G-A		not specified	Uncertain significance (Jan 10, 2023)
11-64340749-T-C		not specified	Uncertain significance (Mar 24, 2023)
11-64340951-A-G		not specified	Uncertain significance (Apr 08, 2024)
11-64340981-T-A		not specified	Uncertain significance (May 31, 2023)
11-64341273-A-C		not specified	Uncertain significance (May 15, 2023)
11-64341421-T-C		not specified	Uncertain significance (Jan 04, 2024)
11-64341445-C-T		not specified	Uncertain significance (May 02, 2024)
11-64341464-G-T		not specified	Uncertain significance (Jul 13, 2021)
11-64341477-G-C		not specified	Uncertain significance (Jan 18, 2022)
11-64341621-T-A		not specified	Uncertain significance (Sep 27, 2022)
11-64341659-G-T		not specified	Uncertain significance (Sep 15, 2021)
11-64341696-T-G		not specified	Uncertain significance (May 04, 2023)
11-64341726-G-A		not specified	Uncertain significance (May 05, 2023)
11-64342040-C-T		not specified	Uncertain significance (Mar 23, 2022)
11-64342048-C-T		not specified	Uncertain significance (Feb 13, 2024)
11-64342057-G-A		not specified	Likely benign (May 30, 2024)
11-64342073-C-T		not specified	Uncertain significance (Jul 13, 2021)
11-64342116-G-T		not specified	Uncertain significance (Feb 13, 2024)
11-64342120-C-T		not specified	Uncertain significance (May 22, 2023)
11-64342129-C-T		not specified	Uncertain significance (Oct 06, 2022)
11-64342130-G-A		not specified	Uncertain significance (Sep 13, 2023)
11-64342565-G-A		not specified	Uncertain significance (May 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC88B	protein_coding	protein_coding	ENST00000356786	27	17312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.40e-9	1.00	125658	0	88	125746	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.943	777	855	0.909	0.0000570	9164
Missense in Polyphen		265	297.19	0.89169		3159
Synonymous	1.38	340	374	0.909	0.0000227	3196
Loss of Function	4.92	29	74.9	0.387	0.00000389	827

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000418	0.000397
Ashkenazi Jewish	0.000119	0.0000992
East Asian	0.000459	0.000326
Finnish	0.000242	0.000231
European (Non-Finnish)	0.000471	0.000440
Middle Eastern	0.000459	0.000326
South Asian	0.000502	0.000490
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a positive regulator of T-cell maturation and inflammatory function. Required for several functions of T-cells, in both the CD4(+) and the CD8(+) compartments and this includes expression of cell surface markers of activation, proliferation, and cytokine production in response to specific or non-specific stimulation (By similarity). Enhances NK cell cytotoxicity by positively regulating polarization of microtubule-organizing center (MTOC) to cytotoxic synapse, lytic granule transport along microtubules, and dynein-mediated clustering to MTOC (PubMed:25762780). Interacts with HSPA5 and stabilizes the interaction between HSPA5 and ERN1, leading to suppression of ERN1-induced JNK activation and endoplasmic reticulum stress- induced apoptosis (PubMed:21289099). {ECO:0000250|UniProtKB:Q4QRL3, ECO:0000269|PubMed:21289099, ECO:0000269|PubMed:25762780}.

Intolerance Scores

• loftool: 0.772
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.432
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.782

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc88b
• Phenotype: immune 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); hematopoietic system phenotype

Gene ontology

• Biological process: positive regulation of cytokine production;cytoskeleton-dependent intracellular transport;cytoplasmic microtubule organization;positive regulation of T cell proliferation;defense response to protozoan;positive regulation of T cell activation
• Cellular component: cytoplasm;endoplasmic reticulum;Golgi apparatus;centrosome;membrane
• Molecular function: microtubule binding;dynein light intermediate chain binding