LSG1

protein-coding

large 60S subunit nuclear export GTPase 1

Gene summary

This gene encodes a protein related to the yeast large subunit GTPase 1. The encoded protein is necessary for cell viability and may localize in the endoplasmic reticulum, nucleus and cytoplasm.[provided by RefSeq, Feb 2009]

MANE transcript

NM_018385.3

Inheritance

—

ClinVar variants

U:135B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr3:194,640,791-194,672,463

External References & Databases

Ensembl (ENSG00000041802)

Transcript & Mutation Effects

hg38 • Region Span ~31.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LSG1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 124

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018385.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	2 clinvar	1 clinvar	8
missense			123 clinvar	6 clinvar		129
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	135	8	1	144

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018385.3	RefSeq	NP_060855.2	14	MANE Select
ENST00000265245.10	Ensembl	ENSP00000265245.5	14	MANE Select
ENST00000427461.1	Ensembl	ENSP00000400903.1	6	Standard
ENST00000437613.1	Ensembl	ENSP00000408264.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)

Biological Process

protein transport
nuclear export

Molecular Function

GTPase activity
GTP binding

Cellular Component

nucleus
endoplasmic reticulum
cytosol
Cajal body
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265245
Coding exons: 14
Length: 31690
Individuals with no LoFs: 125615
Homozygous LoFs: 0
Heterozygous LoFs: 133
Defined: 125748
p: 0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.335	351	369	0.951	0.0000196	4360
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00078	0.00078	rare
Ashkenazi Jewish	0.0025	0.0025	notable
East Asian	0.00022	0.00022	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00047	0.00047	rare
South Asian	0.00030	0.00029	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0974

Intolerance Scores

LoFtool: 0.616
RVIS EVS: 0.43
RVIS percentile EVS: 77.31

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.0442

Gene Damage Prediction

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