ZG16B

protein-coding

zymogen granule protein 16B

Gene summary

Enables proteoglycan binding activity. Involved in several processes, including defense response to bacterium; positive regulation of angiogenesis; and positive regulation of vascular permeability. Located in apicolateral plasma membrane; cytoplasm; and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_145252.3

Inheritance

—

ClinVar variants

U:32B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.09

Max pathogenic AF

—

Genomic locus

chr16:2,830,253-2,839,585

External References & Databases

Ensembl (ENSG00000162078)

Transcript & Mutation Effects

hg38 • Region Span ~9.3 kb

Loading mutation effect viewer...

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 ZG16B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 33

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145252.3. 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			30 clinvar	2 clinvar		32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	32	3	0	35

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145252.3	RefSeq	NP_660295.3	3	MANE Select
ENST00000382280.8	Ensembl	ENSP00000371715.4	3	MANE Select
ENST00000570670.6	Ensembl	ENSP00000460793.2	3	Standard
ENST00000570670.7	Ensembl	ENSP00000460793.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

retina homeostasis

Molecular Function

molecular_function
carbohydrate binding

Cellular Component

extracellular space
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382280
Coding exons: 4
Length: 8798
Individuals with no LoFs: 124610
Homozygous LoFs: 1
Heterozygous LoFs: 151
Defined: 124762
p: 0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.434	136	122	1.11	0.00000695	1323
Missense (PolyPhen)		25	27.884	0.89658		319
Synonymous	0.245	45	47.1	0.955	0.00000256	434
Loss of Function	-0.171	5	4.60	1.09	1.95e-7	56

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0060	0.0055	notable
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.00072	0.00069	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.713
RVIS EVS: 0.51
RVIS percentile EVS: 80.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.107

Gene Damage Prediction

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