ZG16

zymogen granule protein 16

Basic information

Region (hg38): 16:29778256-29782973

Previous symbols: [ "JCLN" ]

Links

ENSG00000174992 ∙ NCBI:653808 ∙ OMIM:617311 ∙ HGNC:30961 ∙ Uniprot:O60844 ∙ 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 ZG16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZG16 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	11	0	1

Variants in ZG16

This is a list of pathogenic ClinVar variants found in the ZG16 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-29779279-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-29779288-G-A		not specified	Uncertain significance (Jun 11, 2021)
16-29779316-A-G		not specified	Uncertain significance (Jun 02, 2024)
16-29779606-C-G		not specified	Uncertain significance (Dec 05, 2022)
16-29779607-G-A		not specified	Uncertain significance (Jul 26, 2021)
16-29779608-GGTCCGA-G			Benign (Jul 06, 2018)
16-29779613-G-A		not specified	Uncertain significance (Feb 17, 2022)
16-29780104-T-A			Benign (Jul 06, 2018)
16-29780177-C-A		not specified	Uncertain significance (Jan 24, 2023)
16-29780277-G-A		not specified	Uncertain significance (May 18, 2023)
16-29780288-G-A		not specified	Uncertain significance (May 30, 2023)
16-29780306-G-A		not specified	Uncertain significance (Feb 05, 2024)
16-29780325-C-A		not specified	Uncertain significance (Dec 11, 2023)
16-29780343-G-C		not specified	Uncertain significance (Mar 18, 2024)
16-29780369-G-A		not specified	Uncertain significance (Sep 29, 2023)
16-29780400-G-G			Benign (Jul 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZG16	protein_coding	protein_coding	ENST00000400752	3	3536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.621	0.372	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	64	102	0.630	0.00000618	1049
Missense in Polyphen		26	43.07	0.60366		410
Synonymous	1.53	30	42.7	0.702	0.00000255	353
Loss of Function	2.17	1	7.33	0.136	4.79e-7	78

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in protein trafficking. May act as a linker molecule between the submembranous matrix on the luminal side of zymogen granule membrane (ZGM) and aggregated secretory proteins during granule formation in the TGN. {ECO:0000269|PubMed:17307141}.

Intolerance Scores

• rvis_EVS: 0.92
• rvis_percentile_EVS: 89.61

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zg16
• Phenotype: immune system phenotype; digestive/alimentary phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein transport
• Cellular component: Golgi lumen;zymogen granule membrane;cytoplasmic vesicle lumen;collagen-containing extracellular matrix
• Molecular function: protein binding;carbohydrate binding