LSM1

LSM1 homolog, mRNA degradation associated, the group of LSm proteins

Basic information

Region (hg38): 8:38163335-38176730

Links

ENSG00000175324 ∙ NCBI:27257 ∙ OMIM:607281 ∙ HGNC:20472 ∙ Uniprot:O15116 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 6.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000311351.9	ENSP00000310596.4	4	yes	-
ENST00000520755.5	ENSP00000430021.1	3	-	-
ENST00000523511.1	ENSP00000428307.1	3	-	-
ENST00000906731.1	ENSP00000576790.1	4	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LSM1 gene.

• not_specified (15 variants)
• not_provided (1 variants)
• Strabismus (1 variants)
• Fetal_pyelectasis (1 variants)
• Generalized_hypotonia (1 variants)
• Hemivertebrae (1 variants)
• Triphalangeal_thumb (1 variants)
• Cryptorchidism (1 variants)
• Global_developmental_delay (1 variants)
• Neurodevelopmental_delay (1 variants)
• Penile_hypospadias (1 variants)
• Intellectual_disability (1 variants)
• Complex_neurodevelopmental_disorder (1 variants)
• Perimembranous_ventricular_septal_defect (1 variants)
• Patent_ductus_arteriosus_after_premature_birth (1 variants)
• Feeding_difficulties (1 variants)
• Hydroureter (1 variants)
• Oligohydramnios (1 variants)
• Inguinal_hernia (1 variants)
• Abnormal_facial_shape (1 variants)
• Bicuspid_aortic_valve (1 variants)
• FICUS_syndrome (1 variants)
• Mitral_stenosis (1 variants)
• Constipation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014462.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense		1	15			16
nonsense						0
start loss			1			1
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	1	19	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSM1	protein_coding	protein_coding	ENST00000311351	4	13410

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125738	0	7	125745	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	48	71.9	0.668	0.00000359	862
Missense in Polyphen		14	22.173	0.63141		262
Synonymous	0.554	22	25.6	0.861	0.00000120	262
Loss of Function	1.20	4	7.57	0.528	4.53e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000665	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the degradation of histone mRNAs, the only eukaryotic mRNAs that are not polyadenylated (PubMed:18172165). Probably also part of an LSm subunits- containing complex involved in the general process of mRNA degradation (By similarity). {ECO:0000250|UniProtKB:P47017, ECO:0000269|PubMed:18172165}.
• Pathway: RNA degradation - Homo sapiens (human);Metabolism of RNA;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Gene ontology

• Biological process: deadenylation-dependent decapping of nuclear-transcribed mRNA;RNA splicing, via transesterification reactions;mRNA processing;RNA splicing;RNA metabolic process;stem cell population maintenance;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;negative regulation of neuron differentiation;histone mRNA catabolic process
• Cellular component: P-body;nucleus;cytoplasm;cytosol;axon;dendrite;neuronal cell body;messenger ribonucleoprotein complex;Lsm1-7-Pat1 complex
• Molecular function: RNA cap binding;RNA binding;mRNA binding;protein binding;pre-mRNA binding