GEMIN2

gem nuclear organelle associated protein 2, the group of Gemins

Basic information

Region (hg38): 14:39114285-39136973

Previous symbols: [ "SIP1" ]

Links

ENSG00000092208 ∙ NCBI:8487 ∙ OMIM:602595 ∙ HGNC:10884 ∙ Uniprot:O14893 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GEMIN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GEMIN2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	10	1	0

Variants in GEMIN2

This is a list of pathogenic ClinVar variants found in the GEMIN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-39114316-C-T		not specified	Likely benign (Dec 21, 2022)
14-39114380-G-T		not specified	Uncertain significance (Jun 16, 2023)
14-39118015-C-A		not specified	Uncertain significance (Dec 01, 2023)
14-39118035-C-G		not specified	Uncertain significance (Oct 30, 2023)
14-39118038-A-G		not specified	Uncertain significance (Nov 06, 2023)
14-39118048-G-C		not specified	Uncertain significance (May 25, 2022)
14-39122521-G-C		not specified	Uncertain significance (Mar 25, 2024)
14-39128295-G-A		not specified	Uncertain significance (Nov 28, 2023)
14-39128333-C-G		not specified	Uncertain significance (Dec 31, 2023)
14-39132040-G-A		not specified	Uncertain significance (Feb 28, 2023)
14-39132067-T-A		not specified	Uncertain significance (Jan 23, 2024)
14-39136460-T-C		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GEMIN2	protein_coding	protein_coding	ENST00000308317	10	22751

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000150	0.858	125704	0	42	125746	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.120	150	146	1.03	0.00000684	1800
Missense in Polyphen		41	44.716	0.9169		540
Synonymous	-0.406	56	52.3	1.07	0.00000250	517
Loss of Function	1.49	12	19.0	0.631	8.73e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000597	0.000569
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000154	0.000139
European (Non-Finnish)	0.000232	0.000220
Middle Eastern	0.0000544	0.0000544
South Asian	0.000117	0.0000980
Other	0.00	0.00

dbNSFP

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, ECO:0000269|PubMed:9323129}.
• Pathway: RNA transport - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;snRNP Assembly;Metabolism of RNA;Metabolism of non-coding RNA (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.130
• hipred: Y
• hipred_score: 0.518
• ghis: 0.632

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Gemin2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: gemin2
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: spliceosomal complex assembly;RNA splicing, via transesterification reactions;spliceosomal snRNP assembly;mRNA processing;RNA splicing;import into nucleus
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;nucleolus;cytoplasm;cytosol;nuclear body;SMN complex;SMN-Sm protein complex;Gemini of coiled bodies
• Molecular function: protein binding