ZGLP1
protein-codingzinc finger GATA like protein 1, the group of GATA zinc finger domain containing
Gene summary
ZGLP1 encodes an evolutionary conserved transcriptional regulator with GATA-like zinc fingers. In females, it is expressed in embryonic germ cells and is essential for oogenic fate determination. It acts downstream of bone morphogenetic protein (BMP) and is involved in the regulation of genes involved in RNA processing, transcription and chromatin modification, retrotransposon regulation, meiotic cell cycle, and oocyte development. In males it is not required for the germ cell sex determination but is required by the spermatogonia for efficiently completing the meiotic prophase. [provided by RefSeq, Jul 2022]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.1 kbGenCC 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 ZGLP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001409033.1. 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 | 0 | |||||
| missense | 31 | 3 | 34 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 31 | 3 | 0 | 34 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001395962.1 | 5 | MANE Select | |
| Ensembl | ENSP00000516709.1 | 5 | MANE Select | |
| RefSeq | NP_001096637.1 | 4 | Standard | |
| Ensembl | ENSP00000385403.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of transcription by RNA polymerase II
- multicellular organism development
- spermatogenesis
- oocyte development
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- zinc ion binding
- sequence-specific DNA binding
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000403903
- Coding exons
- 4
- Length
- 5078
- Individuals with no LoFs
- 117296
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 117297
- p
- 0.00000426
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.25 | 120 | 165 | 0.726 | 0.0000102 | 1703 |
| Missense (PolyPhen) | 14 | 43.662 | 0.32064 | 437 | ||
| Synonymous | 0.331 | 64 | 67.5 | 0.949 | 0.00000426 | 576 |
| Loss of Function | 2.20 | 2 | 9.18 | 0.218 | 3.91e-7 | 104 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcriptional repressor that plays a central role in somatic cells of the gonad and is required for germ cell development. Able to repress GATA transcription factor function (By similarity). {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.312
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.56
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |