ZG16

protein-coding

zymogen granule protein 16

Gene summary

Predicted to enable carbohydrate binding activity and peptidoglycan binding activity. Predicted to be involved in protein transport. Predicted to act upstream of or within defense response to Gram-positive bacterium and suppression of symbiont entry into host. Located in Golgi lumen and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

JCLN

MANE transcript

NM_152338.4

Inheritance

—

ClinVar variants

U:27B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr16:29,778,256-29,782,973

External References & Databases

Ensembl (ENSG00000174992)

Transcript & Mutation Effects

hg38 • Region Span ~4.7 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 ZG16 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152338.4. 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					1 clinvar	1
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	0	1	28

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152338.4	RefSeq	NP_689551.3	3	MANE Select
ENST00000400752.6	Ensembl	ENSP00000383563.4	3	MANE Select
ENST00000897713.1	Ensembl	ENSP00000567772.1	3	Standard
ENST00000897713.2	Ensembl	ENSP00000567772.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport

Molecular Function

protein binding
carbohydrate binding

Cellular Component

Golgi lumen
zymogen granule membrane
cytoplasmic vesicle lumen
collagen-containing extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000400752
Coding exons: 3
Length: 3536
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.33	64	102	0.630	0.00000618	1049
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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 (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.252

Gene Damage Prediction

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