CCZ1

CCZ1 homolog, vacuolar protein trafficking and biogenesis associated

Basic information

Region (hg38): 7:5898725-5926550

Previous symbols: [ "C7orf28A" ]

Links

ENSG00000122674 ∙ NCBI:51622 ∙ ∙ HGNC:21691 ∙ Uniprot:P86791 ∙ 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 CCZ1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCZ1 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			30	1	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			6			6
Total	0	0	36	2	1

Variants in CCZ1

This is a list of pathogenic ClinVar variants found in the CCZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-5898810-C-T		not specified	Uncertain significance (Oct 12, 2022)
7-5898861-C-T		not specified	Uncertain significance (Jan 17, 2024)
7-5900505-T-C		not specified	Uncertain significance (Dec 20, 2023)
7-5900535-A-G		not specified	Uncertain significance (Sep 01, 2021)
7-5900544-A-G		not specified	Uncertain significance (Oct 26, 2022)
7-5900557-G-C		not specified	Uncertain significance (Jun 28, 2023)
7-5900858-G-A		not specified	Uncertain significance (Jan 26, 2022)
7-5900915-C-G		not specified	Uncertain significance (Aug 08, 2022)
7-5901696-A-G		not specified	Uncertain significance (Dec 12, 2023)
7-5905106-C-G		not specified	Uncertain significance (Apr 13, 2022)
7-5905161-C-T		not specified	Uncertain significance (Dec 19, 2023)
7-5905197-T-G		not specified	Uncertain significance (Jan 18, 2023)
7-5905234-A-C		not specified	Uncertain significance (Jun 22, 2023)
7-5905242-C-T		not specified	Uncertain significance (Jun 28, 2022)
7-5910036-A-G		not specified	Uncertain significance (Mar 14, 2023)
7-5910088-C-A		not specified	Uncertain significance (Sep 16, 2021)
7-5910112-C-G		not specified	Uncertain significance (Mar 01, 2023)
7-5911886-G-A		not specified	Uncertain significance (Aug 21, 2023)
7-5912871-G-A		not specified	Uncertain significance (Oct 20, 2023)
7-5912898-A-C		not specified	Uncertain significance (Oct 25, 2022)
7-5912899-A-G		not specified	Uncertain significance (Mar 04, 2024)
7-5912923-C-T		not specified	Uncertain significance (Jun 06, 2023)
7-5912947-T-C		not specified	Uncertain significance (Sep 06, 2022)
7-5919854-G-A			Benign (Jun 22, 2017)
7-5919879-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCZ1	protein_coding	protein_coding	ENST00000325974	15	27250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000359	0.948	125709	4	33	125746	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.194	199	191	1.04	0.00000990	3181
Missense in Polyphen		50	51.002	0.98035		869
Synonymous	-0.867	79	69.8	1.13	0.00000405	798
Loss of Function	1.83	12	21.1	0.569	8.86e-7	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000542	0.000463
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000530	0.0000462
European (Non-Finnish)	0.000320	0.000220
Middle Eastern	0.00	0.00
South Asian	0.0000668	0.0000653
Other	0.000182	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts in concert with MON1A, as a guanine exchange factor (GEF) for RAB7, promotes the exchange of GDP to GTP, converting it from an inactive GDP-bound form into an active GTP-bound form (PubMed:23084991). {ECO:0000269|PubMed:23084991}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.203
• hipred: N
• hipred_score: 0.455
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccz1

Gene ontology

• Biological process: vesicle-mediated transport
• Cellular component: lysosomal membrane;cytosol;aggresome;Mon1-Ccz1 complex;intracellular membrane-bounded organelle
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding