LSG1

large 60S subunit nuclear export GTPase 1

Basic information

Region (hg38): 3:194640791-194672463

Links

ENSG00000041802 ∙ NCBI:55341 ∙ OMIM:610780 ∙ HGNC:25652 ∙ Uniprot:Q9H089 ∙ 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 LSG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSG1 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				2	1	3
missense			61	4		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	61	6	1

Variants in LSG1

This is a list of pathogenic ClinVar variants found in the LSG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-194642075-T-A		not specified	Uncertain significance (Aug 12, 2021)
3-194642080-G-C		not specified	Uncertain significance (Jul 09, 2021)
3-194642084-T-C		not specified	Uncertain significance (Mar 07, 2023)
3-194642096-C-T		not specified	Uncertain significance (Dec 22, 2023)
3-194642097-G-C		not specified	Uncertain significance (Jul 27, 2023)
3-194642098-A-C		not specified	Uncertain significance (Jan 27, 2022)
3-194642099-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-194642147-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-194642165-G-A		not specified	Likely benign (Jul 09, 2021)
3-194642165-G-T		not specified	Uncertain significance (Apr 20, 2023)
3-194642194-G-A			Likely benign (Jun 06, 2018)
3-194644596-C-T		not specified	Uncertain significance (Aug 16, 2022)
3-194644636-C-A		not specified	Uncertain significance (Sep 01, 2021)
3-194644649-T-C		not specified	Uncertain significance (Aug 13, 2021)
3-194644727-T-C		not specified	Uncertain significance (Dec 15, 2023)
3-194644731-A-C		not specified	Uncertain significance (May 07, 2024)
3-194646190-G-A		not specified	Uncertain significance (Feb 15, 2023)
3-194646228-A-G		not specified	Uncertain significance (May 03, 2023)
3-194646248-GGA-G			Benign (Jun 13, 2018)
3-194648692-G-T		not specified	Uncertain significance (Feb 16, 2023)
3-194648694-C-G		not specified	Uncertain significance (Jun 29, 2022)
3-194648714-G-A		not specified	Uncertain significance (Jul 25, 2023)
3-194648719-C-T		not specified	Uncertain significance (Jul 13, 2022)
3-194648745-C-T			Benign (May 21, 2018)
3-194648753-T-C		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSG1	protein_coding	protein_coding	ENST00000265245	14	31690

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.55e-12	0.931	125615	0	133	125748	0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.335	351	369	0.951	0.0000196	4360
Missense in Polyphen		93	105.89	0.87825		1217
Synonymous	-0.0900	136	135	1.01	0.00000765	1210
Loss of Function	2.07	24	37.7	0.636	0.00000209	407

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00103
Ashkenazi Jewish	0.00248	0.00248
East Asian	0.000218	0.000217
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000469	0.000466
Middle Eastern	0.000218	0.000217
South Asian	0.000298	0.000294
Other	0.000823	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase required for the XPO1/CRM1-mediated nuclear export of the 60S ribosomal subunit. Probably acts by mediating the release of NMD3 from the 60S ribosomal subunit after export into the cytoplasm (Probable). {ECO:0000305|PubMed:16209721}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.616
• rvis_EVS: 0.43
• rvis_percentile_EVS: 77.31

Haploinsufficiency Scores

• pHI: 0.134
• hipred: Y
• hipred_score: 0.648
• ghis: 0.519

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0442

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lsg1

Gene ontology

• Biological process: protein transport;nuclear export
• Cellular component: nucleus;endoplasmic reticulum;cytosol;Cajal body;membrane;nuclear body
• Molecular function: GTPase activity;GTP binding