GEMIN6

gem nuclear organelle associated protein 6, the group of Gemins

Basic information

Region (hg38): 2:38751534-38785002

Links

ENSG00000152147 ∙ NCBI:79833 ∙ OMIM:607006 ∙ HGNC:20044 ∙ Uniprot:Q8WXD5 ∙ 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 GEMIN6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GEMIN6 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in GEMIN6

This is a list of pathogenic ClinVar variants found in the GEMIN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-38779004-T-C		not specified	Uncertain significance (Nov 18, 2022)
2-38779026-G-T		not specified	Uncertain significance (Jan 23, 2024)
2-38779105-C-T		not specified	Uncertain significance (Aug 01, 2022)
2-38781545-G-A		not specified	Uncertain significance (May 24, 2023)
2-38781586-G-T		not specified	Uncertain significance (Oct 13, 2023)
2-38781611-G-A		not specified	Uncertain significance (Aug 23, 2021)
2-38781621-T-C		not specified	Uncertain significance (Mar 30, 2022)
2-38781727-C-A		not specified	Uncertain significance (Jan 04, 2024)
2-38781758-C-G		not specified	Uncertain significance (Jan 10, 2023)
2-38781797-C-T		not specified	Uncertain significance (Sep 06, 2023)
2-38781828-C-G		not specified	Uncertain significance (Oct 14, 2023)
2-38781838-T-G		not specified	Uncertain significance (Dec 28, 2023)
2-38781842-C-G		not specified	Uncertain significance (Mar 15, 2024)
2-38781846-C-T		not specified	Uncertain significance (Dec 14, 2023)
2-38781851-G-T		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GEMIN6	protein_coding	protein_coding	ENST00000281950	2	33467

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000106	0.378	125723	0	23	125746	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.92	143	91.4	1.57	0.00000443	1105
Missense in Polyphen		46	31.625	1.4545		385
Synonymous	-0.712	38	32.8	1.16	0.00000178	309
Loss of Function	0.0522	6	6.14	0.977	3.10e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.000163	0.000163

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:11748230, ECO:0000269|PubMed:18984161}.
• Pathway: RNA transport - Homo sapiens (human);snRNP Assembly;Metabolism of RNA;Metabolism of non-coding RNA (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.666
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.123
• hipred: Y
• hipred_score: 0.767
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gemin6

Gene ontology

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