GEMIN7

gem nuclear organelle associated protein 7, the group of Gemins

Basic information

Region (hg38): 19:45079195-45091518

Links

ENSG00000142252 ∙ NCBI:79760 ∙ OMIM:607419 ∙ HGNC:20045 ∙ Uniprot:Q9H840 ∙ 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 GEMIN7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GEMIN7 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in GEMIN7

This is a list of pathogenic ClinVar variants found in the GEMIN7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-45090133-A-G		not specified	Uncertain significance (May 30, 2024)
19-45090164-G-T		not specified	Uncertain significance (May 14, 2024)
19-45090198-T-A		not specified	Uncertain significance (Nov 13, 2023)
19-45090230-C-T		not specified	Uncertain significance (Oct 05, 2022)
19-45090254-C-T		not specified	Likely benign (Aug 17, 2022)
19-45090262-T-A		not specified	Uncertain significance (Feb 14, 2023)
19-45090420-C-G		not specified	Uncertain significance (May 31, 2023)
19-45090457-G-A		not specified	Uncertain significance (Nov 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GEMIN7	protein_coding	protein_coding	ENST00000270257	1	12330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.645	0.330	125728	0	10	125738	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.347	82	91.3	0.898	0.00000621	825
Missense in Polyphen		34	35.349	0.96183		314
Synonymous	1.17	28	37.0	0.756	0.00000232	301
Loss of Function	1.69	0	3.34	0.00	2.42e-7	26

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
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:12065586, ECO:0000269|PubMed:18984161}.
• Pathway: RNA transport - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;snRNP Assembly;Metabolism of RNA;Metabolism of non-coding RNA (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.245
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.135
• hipred: Y
• hipred_score: 0.552
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gemin7

Gene ontology

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