GEMIN4
protein-codinggem nuclear organelle associated protein 4, the group of Minor histocompatibility antigens|Gemins
Gene summary
The product of this gene is part of a large complex localized to the cytoplasm, nucleoli, and to discrete nuclear bodies called Gemini bodies (gems). The complex functions in spliceosomal snRNP assembly in the cytoplasm, and regenerates spliceosomes required for pre-mRNA splicing in the nucleus. The encoded protein directly interacts with a DEAD box protein and several spliceosome core proteins. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0060664
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0060664
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0060664
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0060664
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Neurologic; Ophthalmologic; Renal
Intervention: Renal
Rationale: The condition can include renal manifestations, including hydronephrosis, renal stones, nephrocalcinosis, and secondary hypertension, and awareness may allow early management of renal-related manifestations
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GEMIN4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015721.3. 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 | 1 | 40 | 4 | 45 | ||
| missense | 1 | 1 | 209 | 27 | 7 | 245 |
| nonsense | 7 | 7 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 5 | 7 | |||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 3 | 222 | 67 | 11 | 304 |
Highest pathogenic variant AF is 0.00005579188
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056536.2 | 2 | MANE Select | |
| Ensembl | ENSP00000321706.5 | 2 | MANE Select | |
| Ensembl | ENSP00000392460.1 | 3 | Standard | |
| Ensembl | ENSP00000392460.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA transport - Homo sapiens (human)
- snRNP Assembly
- Metabolism of RNA
- Metabolism of non-coding RNA
Biological Process
- spliceosomal snRNP assembly
- rRNA processing
- import into nucleus
Molecular Function
- protein binding
Cellular Component
- nucleoplasm
- nucleolus
- cytoplasm
- cytosol
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000319004
- Coding exons
- 2
- Length
- 9586
- Individuals with no LoFs
- 124514
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 187
- Defined
- 124701
- p
- 0.000750
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.468 | 626 | 594 | 1.05 | 0.0000357 | 6872 |
| Missense (PolyPhen) | 212 | 195.88 | 1.0823 | 2584 | ||
| Synonymous | -1.37 | 293 | 265 | 1.11 | 0.0000175 | 2176 |
| Loss of Function | 1.52 | 24 | 33.5 | 0.716 | 0.00000171 | 372 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00039 | 0.00039 | rare |
| Latino/Admixed American | 0.00084 | 0.00084 | rare |
| Ashkenazi Jewish | 0.00041 | 0.00040 | rare |
| East Asian | 0.00089 | 0.00089 | rare |
| Finnish | 0.00076 | 0.00074 | rare |
| European (Non-Finnish) | 0.00067 | 0.00065 | rare |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.0010 | 0.00099 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. {ECO:0000269|PubMed:18984161}.;
- Disease
- DISEASE: Neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalities (NEDMCR) [MIM:617913]: An autosomal recessive, severe neurodevelopmental disorder characterized by global developmental delay since infancy, microcephaly, poor or absent speech, and inability to walk or spasticity. Additional features include renal abnormalities, congenital cataracts, gastroesophageal reflux disease, seizures with onset in infancy or childhood, hyporeflexia, and non-specific white matter abnormalities on brain imaging. {ECO:0000269|PubMed:25558065}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- LoFtool
- 0.936
- RVIS EVS
- 3.4
- RVIS percentile EVS
- 99.45
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.753
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |