GEMIN5
protein-codinggem nuclear organelle associated protein 5, the group of WD repeat domain containing|Gemins
Gene summary
This gene encodes a WD repeat protein that is a component of the survival of motor neurons (SMN) complex. The SMN complex plays a critical role in mRNA splicing through the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs), and may also mediate the assembly and transport of other classes of ribonucleoproteins. The encoded protein is the snRNA-binding component of the SMN complex. Dysregulation of this gene may play a role in alternative mRNA splicing and tumor cell motility. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0859152
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0859152
Submitter: ClinGen
The *GEMIN5* gene is located on chromosome 5 at 5q33.2 and encodes for a predominantly cytoplasmic protein that is a component of the survival of motor neurons (SMN) complex which is involved in the assembly and biogenesis of small nuclear ribonucleoproteins (snRNPs), the building blocks of the splicing machinery (PMIDs: 16857593, 18984161 and 20513430). Outside of the spliceosome, GEMIN5 has other functional roles including as a regulator of translation, ribosome-interacting protein, reprogramming factor in hair cells, signal recognition particle-interacting protein, and trans-splicing factor (PMIDs: 19066202, 25911097, 29771365, 32218991 and 23221635). GEMIN5 is expressed ubiquitously at the RNA and protein level (PMID: 28940711). Biallelic variants in *GEMIN5* were first reported in 2021 in association with a neurodevelopmental disorder with cerebellar atrophy and motor dysfunction (NEDCAM), in 30 affected individuals from 22 unrelated families (Kour et al., PMID: 33963192). Phenotypic features include motor-predominant developmental delay, diagnosed within 2 years of life, and cerebellar atrophy on brain MRI. Most patients had non-progressive cognitive and speech delays, while some patients had central hypotonia, with variable muscle tone, deep tendon reflexes, and walking ability. The clinical course was mostly static, though some experienced progression. NEDCAM has been stratified into three subgroups, based on age of onset and severity (Rajan et al., 2022, PMID:35295849). In total, 11 biallelic variants (3 LOF, and 7 non-recurrent and 1 recurrent missense) from 7 unrelated families with 9 affected individuals with spastic ataxia and cerebellar atrophy were included in this curation. Additional variants have also been reported from various case studies, some of which include rarer congenital hypothyroidism and infantile spasm phenotypes; further highlighting the wide clinical spectrum and variable severity of NEDCAM (PMIDs: 34569062, 37479787 and 36980979). The proposed mechanism of disease is biallelic loss of function. This gene-disease relationship is also supported by experimental evidence including expression and non-human model organisms (Drosophila, zebrafish). On the variant level, *GEMIN5* variants in patient-derived iPSC neurons and lymphoblastoid cell lines show a reduction in protein expression, which in turns led to reduced protein and SMN complex interactions, ribosome dissociation and translation dysregulation (PMIDs: 35393353 and 34569062). On the gene level, the loss of *GEMIN5* has been studied in Drosophila and Zebrafish homologues, which recapitulated the developmental delay and motor dysfunction, and dysplastic cerebellum observed in NEDCAM respectively (PMIDs: 33963192 and 34569062). In summary, there is definitive evidence supporting the relationship between *GEMIN5* and NEDCAM. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the Syndromic Disorders GCEP on September 6, 2023 (SOP Version 9).
Inheritance Pattern: AR
Disease ID:MONDO:0859152
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0859152
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GEMIN5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015465.5. 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 | 21 | 22 | |||
| missense | 4 | 6 | 267 | 21 | 4 | 302 |
| nonsense | 4 | 8 | 2 | 1 | 15 | |
| start loss | 0 | |||||
| frameshift | 4 | 5 | 3 | 1 | 13 | |
| splice donor/acceptor (+/-2bp) | 6 | 10 | 16 | |||
| Total | 12 | 25 | 283 | 44 | 4 | 368 |
Highest pathogenic variant AF is 0.0070399987
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056280.2 | 28 | MANE Select | |
| Ensembl | ENSP00000285873.6 | 28 | MANE Select | |
| RefSeq | NP_001239085.1 | 28 | Standard | |
| Ensembl | ENSP00000668277.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| gemin5 | Danio rerio | Structure: thymus Quality: decreased amount abnormal |
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
- mRNA splicing, via spliceosome
- translation
- regulation of translation
- import into nucleus
Molecular Function
- RNA 7-methylguanosine cap binding
- RNA binding
- mRNA 3'-UTR binding
- protein binding
- snRNA binding
Cellular Component
- nucleoplasm
- cytoplasm
- cytosol
- membrane
- nuclear body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000285873
- Coding exons
- 28
- Length
- 50794
- Individuals with no LoFs
- 125600
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 147
- Defined
- 125747
- p
- 0.000585
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0677 | 781 | 786 | 0.993 | 0.0000395 | 9816 |
| Missense (PolyPhen) | 223 | 248.38 | 0.89782 | 3106 | ||
| Synonymous | -0.767 | 314 | 297 | 1.06 | 0.0000155 | 2907 |
| Loss of Function | 3.43 | 47 | 80.1 | 0.587 | 0.00000404 | 948 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0014 | 0.0014 | notable |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00055 | 0.00054 | rare |
| Finnish | 0.00033 | 0.00032 | rare |
| European (Non-Finnish) | 0.00054 | 0.00052 | rare |
| South Asian | 0.0011 | 0.0010 | notable |
| Other | 0.00050 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required for the assembly of the SMN complex that plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:16857593, PubMed:18984161, PubMed:20513430). 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 (PubMed:18984161). 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 (PubMed:18984161). GEMIN5 acts as the snRNA-binding protein of the SMN complex (PubMed:11714716, PubMed:16857593, PubMed:19377484, PubMed:19750007, PubMed:20513430, PubMed:27834343, PubMed:27881600, PubMed:27881601). Binds to the 7-methylguanosine cap of RNA molecules (PubMed:19750007, PubMed:27834343, PubMed:27881600, PubMed:27881601, Ref.25). Binds to the 3'-UTR of SMN1 mRNA and regulates its translation; does not affect mRNA stability (PubMed:25911097). May play a role in the regulation of protein synthesis via its interaction with ribosomes (PubMed:27507887). {ECO:0000269|PubMed:11714716, ECO:0000269|PubMed:16857593, ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:19377484, ECO:0000269|PubMed:19750007, ECO:0000269|PubMed:20513430, ECO:0000269|PubMed:25911097, ECO:0000269|PubMed:27507887, ECO:0000269|PubMed:27834343, ECO:0000269|PubMed:27881600, ECO:0000269|PubMed:27881601, ECO:0000269|Ref.25}.;
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- LoFtool
- 0.948
- RVIS EVS
- 0.22
- RVIS percentile EVS
- 68.14
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.702
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |