PLCZ1

Chr 12AR

phospholipase C zeta 1

Also known as: Czeta, NYD-SP27, PLC-zeta-1, PLCzeta, SPGF17

NCBI Gene: 89869ENSG00000139151UniProt: Q86YW0

This phospholipase C enzyme hydrolyzes phosphatidylinositol 4,5-bisphosphate to produce diacylglycerol and inositol 1,4,5-trisphosphate, and is essential for triggering calcium oscillations during oocyte activation and early embryonic development. Mutations cause spermatogenic failure 17, an autosomal recessive condition affecting male fertility. The gene shows minimal constraint against loss-of-function variants, consistent with its specialized reproductive function.

Summary from RefSeq, OMIM, UniProt
Research Assistant →

Primary Disease Associations & Inheritance

Spermatogenic failure 17MIM #617214
AR
0
Active trials
14
Pubs (1 yr)
52
P/LP submissions
12%
P/LP missense
1.02
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— PLCZ1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
51 unique Pathogenic / Likely Pathogenic· 76 VUS of 144 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.02LOEUF
pLI 0.000
Z-score 1.44
OE 0.72 (0.52–1.02)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.61Z-score
OE missense 1.10 (1.00–1.20)
342 obs / 311.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.72 (0.52–1.02)
0≤0.351.4
Missense OE1.10 (1.00–1.20)
0≤0.61.4
Synonymous OE1.10
0≤1.21.6
LoF obs/exp: 23 / 31.8Missense obs/exp: 342 / 311.8Syn Z: -0.76
DN
0.7035th %ile
GOF
0.7029th %ile
LOF
0.2679th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
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.

ClinVar Variant Classifications

144 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic46
Likely Pathogenic5
VUS76
Likely Benign10
Benign1
46
Pathogenic
5
Likely Pathogenic
76
VUS
10
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
4
39
0
46
Likely Pathogenic
1
2
2
0
5
VUS
1
71
4
0
76
Likely Benign
0
5
1
4
10
Benign
0
1
0
0
1
Total583464138

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PLCZ1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients