ZG16B

Chr 16

zymogen granule protein 16B

Also known as: EECP, HRPE773, JCLN2, PAUF, PRO1567

NCBI Gene: 124220 ENSG00000162078 UniProt: Q96DA0 OMIM: 620477

The ZG16B protein functions as a lectin that binds carbohydrates and helps maintain oral microbiome homeostasis by capturing and regulating commensal bacteria growth. Pathogenic variants in ZG16B cause neurodevelopmental disorders with intellectual disability, seizures, and dysmorphic features, following an autosomal recessive inheritance pattern. The gene shows low constraint to loss-of-function variants (pLI 0.0003, LOEUF 1.85), suggesting tolerance to protein loss.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable carbohydrate binding activity. Involved in cell migration. Located in apicolateral plasma membrane; cytoplasm; and extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

GOFmechanismLOEUF 1.85

Clinical Summary— ZG16B

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.85LOEUF

pLI 0.000

Z-score -0.17

OE 1.09 (0.55–1.85)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.43Z-score

OE missense 1.11 (0.96–1.28)

136 obs / 122.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.09 (0.55–1.85)

0≤0.351.4

Missense OE?1.11 (0.96–1.28)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 5 / 4.6Missense obs/exp: 136 / 122.5Syn Z: 0.24

This gene — mechanism propensity

0.6163th %ile

GOF

0.6542th %ile

LOF

0.3358th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.