ZG16B

zymogen granule protein 16B

Basic information

Region (hg38): 16:2830253-2839585

Links

ENSG00000162078 ∙ NCBI:124220 ∙ ∙ HGNC:30456 ∙ Uniprot:Q96DA0 ∙ 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 ZG16B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZG16B 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	2		3
Total	0	0	15	3	0

Variants in ZG16B

This is a list of pathogenic ClinVar variants found in the ZG16B region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2830299-G-A		not specified	Uncertain significance (May 27, 2022)
16-2830302-A-C		not specified	Uncertain significance (Jul 12, 2023)
16-2830312-G-A		not specified	Likely benign (Dec 13, 2022)
16-2830430-C-T		not specified	Uncertain significance (Nov 02, 2023)
16-2830431-G-A		not specified	Likely benign (Oct 04, 2022)
16-2830720-T-C		not specified	Uncertain significance (Jul 25, 2023)
16-2830742-A-G		not specified	Uncertain significance (Aug 04, 2023)
16-2830774-G-A		not specified	Uncertain significance (Apr 25, 2023)
16-2830795-A-G		not specified	Uncertain significance (Apr 07, 2022)
16-2831796-T-G		not specified	Uncertain significance (Oct 29, 2021)
16-2831797-G-A		not specified	Likely benign (Mar 01, 2024)
16-2831800-C-G		not specified	Uncertain significance (Nov 17, 2022)
16-2831840-C-G		not specified	Uncertain significance (Dec 13, 2023)
16-2831864-T-C		not specified	Uncertain significance (Feb 05, 2024)
16-2831881-G-A		not specified	Uncertain significance (Apr 19, 2024)
16-2831905-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-2831953-C-A		not specified	Uncertain significance (Apr 08, 2024)
16-2831981-G-T		not specified	Uncertain significance (Mar 31, 2023)
16-2832001-C-T		not specified	Uncertain significance (Apr 20, 2023)
16-2832034-T-A		not specified	Uncertain significance (Apr 20, 2023)
16-2832092-T-C		not specified	Uncertain significance (Apr 01, 2024)
16-2832104-C-A		not specified	Uncertain significance (Oct 22, 2021)
16-2832155-G-A		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZG16B	protein_coding	protein_coding	ENST00000382280	4	8798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000300	0.365	124610	1	151	124762	0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.434	136	122	1.11	0.00000695	1323
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000158	0.000158
Ashkenazi Jewish	0.00	0.00
East Asian	0.00601	0.00547
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.000253	0.000247
Middle Eastern	0.00601	0.00547
South Asian	0.000723	0.000686
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.713
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.257
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

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

Gene ontology

• Biological process: retina homeostasis
• Cellular component: extracellular space;extracellular exosome
• Molecular function: molecular_function;carbohydrate binding