GGNBP2

Chr 17

gametogenetin binding protein 2

Also known as: DIF-3, DIF3, LCRG1, LZK1, ZFP403, ZNF403

NCBI Gene: 79893 ENSG00000278311 UniProt: Q9H3C7 OMIM: 612275

The protein is predicted to be involved in spermatogenesis and may regulate cell proliferation and blood vessel development. GGNBP2 is extremely intolerant to loss-of-function variants (pLI ~1.0, LOEUF 0.073), but no established human disease associations have been reported to date.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to be involved in spermatogenesis. Predicted to act upstream of or within several processes, including labyrinthine layer blood vessel development; negative regulation of cell population proliferation; and negative regulation of peptidyl-tyrosine phosphorylation. Predicted to be located in cytoplasmic vesicle. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2025]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.07

Clinical Summary— GGNBP2

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.07LOEUF

pLI 1.000

Z-score 5.92

OE 0.00 (0.00–0.07)

Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?

3.26Z-score

OE missense 0.53 (0.47–0.60)

204 obs / 383.7 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.07)

0≤0.351.4

Missense OE?0.53 (0.47–0.60)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 0 / 40.8Missense obs/exp: 204 / 383.7Syn Z: 0.55

This gene — mechanism propensity

0.2599th %ile

GOF

0.3689th %ile

LOF

0.76top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.07

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.