CCDC88B

protein-coding

coiled-coil domain containing 88B

Gene summary

This gene encodes a member of the hook-related protein family. Members of this family are characterized by an N-terminal potential microtubule binding domain, a central coiled-coiled and a C-terminal Hook-related domain. The encoded protein may be involved in linking organelles to microtubules. [provided by RefSeq, Oct 2009]

Previous symbols:

CCDC88

MANE transcript

NM_032251.6

Inheritance

—

ClinVar variants

U:290B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr11:64,340,204-64,357,534

External References & Databases

Ensembl (ENSG00000168071)

Transcript & Mutation Effects

hg38 • Region Span ~17.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC88B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 284

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032251.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	1 clinvar	1 clinvar	8
missense			282 clinvar	8 clinvar		290
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	290	9	1	300

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032251.6	RefSeq	NP_115627.6	27	MANE Select
ENST00000356786.10	Ensembl	ENSP00000349238.5	27	MANE Select
ENST00000301897.5	Ensembl	ENSP00000301897.4	4	Standard
ENST00000359902.2	Ensembl	ENSP00000352974.2	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of cytokine production
cytoskeleton-dependent intracellular transport
cytoplasmic microtubule organization
positive regulation of T cell proliferation
defense response to protozoan

Molecular Function

microtubule binding
dynein light intermediate chain binding

Cellular Component

cytoplasm
endoplasmic reticulum
Golgi apparatus
centrosome
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356786
Coding exons: 27
Length: 17312
Individuals with no LoFs: 125658
Homozygous LoFs: 0
Heterozygous LoFs: 88
Defined: 125746
p: 0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.943	777	855	0.909	0.0000570	9164
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0.00012	0.000099	rare
East Asian	0.00046	0.00033	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00047	0.00044	rare
South Asian	0.00050	0.00049	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.782

Gene Damage Prediction

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