GEMIN4

protein-coding

gem 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

NM_015721.3

Inheritance

AR

ClinVar variants

P:4U:222B:78

Top phenotype

Neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalities

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr17:744,421-753,999

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~9.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalitiesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060664

Submitter: G2P

neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalitiesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060664

Submitter: Labcorp Genetics (formerly Invitae)

neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalitiesLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0060664

Submitter: Ambry Genetics

neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalitiesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060664

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalitiesAR

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

Refs: 25558065; 27878435; 30237576Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GEMIN4 variants in ClinVar

8 Conditions Cataloged
not specifiedTotal: 217
not providedTotal: 79
GEMIN4-related disorderTotal: 32
Neurodevelopmental disorder with microcephaly, cataracts, and renal abnormalitiesTotal: 19
Developmental cataractTotal: 1
Severe dystoniaTotal: 1
Global developmental delayTotal: 1
MicrocephalyTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
40
clinvar
4
clinvar
45
missense
1
clinvar
1
clinvar
209
clinvar
27
clinvar
7
clinvar
245
nonsense
7
clinvar
7
start loss
0
frameshift
2
clinvar
5
clinvar
7
splice donor/acceptor (+/-2bp)
0
Total132226711304

Highest pathogenic variant AF is 0.00005579188

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015721.3RefSeqNP_056536.22MANE Select
ENST00000319004.6EnsemblENSP00000321706.52MANE Select
ENST00000437269.1EnsemblENSP00000392460.13Standard
ENST00000437269.2EnsemblENSP00000392460.13Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.4686265941.050.00003576872
Missense (PolyPhen)212195.881.08232584
Synonymous-1.372932651.110.00001752176
Loss of Function1.522433.50.7160.00000171372

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000390.00039rare
Latino/Admixed American0.000840.00084rare
Ashkenazi Jewish0.000410.00040rare
East Asian0.000890.00089rare
Finnish0.000760.00074rare
European (Non-Finnish)0.000670.00065rare
South Asian0.00120.0012notable
Other0.00100.00099notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.