GEMIN5

protein-coding

gem 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

NM_015465.5

Inheritance

AR

ClinVar variants

P:37U:283B:48

Top phenotype

Neurodevelopmental disorder with cerebellar atrophy and motor dysfunction

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr5:154,887,411-154,938,211

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~50.8 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorder with cerebellar atrophy and motor dysfunctionSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859152

Submitter: G2P

neurodevelopmental disorder with cerebellar atrophy and motor dysfunctionDEFINITIVE

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).

neurodevelopmental disorder with cerebellar atrophy and motor dysfunctionSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859152

Submitter: PanelApp Australia

neurodevelopmental disorder with cerebellar atrophy and motor dysfunctionSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859152

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with cerebellar atrophy and motor dysfunctionAR

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

Refs: 33963192Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GEMIN5 variants in ClinVar

7 Conditions Cataloged
Inborn genetic diseasesTotal: 233
not providedTotal: 76
Neurodevelopmental disorder with cerebellar atrophy and motor dysfunctionTotal: 47
not specifiedTotal: 22
GEMIN5-related disorderTotal: 9
Essential tremorTotal: 1
GEMIN5-related neurodevelopmental disorderTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
21
clinvar
22
missense
4
clinvar
6
clinvar
267
clinvar
21
clinvar
4
clinvar
302
nonsense
4
clinvar
8
clinvar
2
clinvar
1
clinvar
15
start loss
0
frameshift
4
clinvar
5
clinvar
3
clinvar
1
clinvar
13
splice donor/acceptor (+/-2bp)
6
clinvar
10
clinvar
16
Total1225283444368

Highest pathogenic variant AF is 0.0070399987

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015465.5RefSeqNP_056280.228MANE Select
ENST00000285873.8EnsemblENSP00000285873.628MANE Select
NM_001252156.2RefSeqNP_001239085.128Standard
ENST00000998460.1EnsemblENSP00000668277.18Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
gemin5Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.06777817860.9930.00003959816
Missense (PolyPhen)223248.380.897823106
Synonymous-0.7673142971.060.00001552907
Loss of Function3.434780.10.5870.00000404948

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00140.0014notable
Latino/Admixed American0.000380.00038rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000550.00054rare
Finnish0.000330.00032rare
European (Non-Finnish)0.000540.00052rare
South Asian0.00110.0010notable
Other0.000500.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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