CCZ1B

CCZ1 homolog B, vacuolar protein trafficking and biogenesis associated

Basic information

Region (hg38): 7:6794134-6826770

Previous symbols: [ "C7orf28B" ]

Links

ENSG00000146574 ∙ NCBI:221960 ∙ ∙ HGNC:21717 ∙ Uniprot:P86790 ∙ 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 CCZ1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCZ1B 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
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in CCZ1B

This is a list of pathogenic ClinVar variants found in the CCZ1B region.

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

Position	Type	Phenotype	Significance	ClinVar
7-6796588-G-A		not specified	Uncertain significance (Dec 06, 2024)
7-6796611-C-G		not specified	Uncertain significance (May 07, 2024)
7-6796614-G-A		not specified	Likely benign (Dec 19, 2023)
7-6796695-A-G		not specified	Uncertain significance (Jan 03, 2024)
7-6796711-C-T			Likely benign (Mar 01, 2023)
7-6796715-G-C		not specified	Uncertain significance (Nov 12, 2021)
7-6796715-G-T		not specified	Uncertain significance (Aug 17, 2022)
7-6796730-A-G		not specified	Uncertain significance (Oct 12, 2024)
7-6796735-C-T		not specified	Uncertain significance (Oct 20, 2023)
7-6796736-G-A		not specified	Uncertain significance (Dec 17, 2023)
7-6798381-G-C		not specified	Uncertain significance (Apr 13, 2023)
7-6798470-T-C		not specified	Likely benign (Oct 29, 2021)
7-6798482-A-G		not specified	Uncertain significance (Nov 17, 2023)
7-6798489-T-G		not specified	Uncertain significance (Feb 07, 2025)
7-6799255-G-A		not specified	Uncertain significance (Dec 05, 2024)
7-6799262-A-G		not specified	Uncertain significance (Dec 18, 2023)
7-6800971-T-C		not specified	Uncertain significance (May 28, 2024)
7-6801002-G-A		not specified	Uncertain significance (Aug 04, 2024)
7-6804941-G-A		not specified	Uncertain significance (Dec 03, 2024)
7-6805041-T-G		not specified	Uncertain significance (Dec 03, 2024)
7-6805055-G-C		not specified	Uncertain significance (Feb 06, 2023)
7-6806007-C-T		not specified	Uncertain significance (Oct 26, 2022)
7-6806025-C-T		not specified	Conflicting classifications of pathogenicity (Nov 07, 2024)
7-6811960-C-T		not specified	Uncertain significance (Feb 23, 2023)
7-6812026-C-T		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCZ1B	protein_coding	protein_coding	ENST00000316731	15	32637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.97e-13	0.0754	125705	1	29	125735	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.350	178	192	0.929	0.00000971	3205
Missense in Polyphen		35	49.408	0.70839		868
Synonymous	0.651	62	68.9	0.900	0.00000391	802
Loss of Function	0.484	20	22.5	0.890	0.00000102	357

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000392	0.000382
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.0000925	0.0000791
Middle Eastern	0.000218	0.000217
South Asian	0.000141	0.000131
Other	0.000202	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Intolerance Scores

• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.02

Haploinsufficiency Scores

• pHI: 0.243
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: vesicle-mediated transport
• Cellular component: lysosomal membrane;cytosol;aggresome;Mon1-Ccz1 complex;intracellular membrane-bounded organelle