LSM10

LSM10, U7 small nuclear RNA associated, the group of LSm proteins

Basic information

Region (hg38): 1:36391238-36397908

Links

ENSG00000181817

∙ NCBI:84967 ∙ OMIM:617909 ∙ HGNC:17562 ∙ Uniprot:Q969L4 ∙ 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 LSM10 gene.

not_specified (14 variants)
Fraser_syndrome_3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032881.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSM10	protein_coding	protein_coding	ENST00000315732	1	6655

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00407	0.435	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.468	72	84.1	0.856	0.00000626	801
Missense in Polyphen		28	32.308	0.86665		290
Synonymous	-0.305	35	32.8	1.07	0.00000205	260
Loss of Function	-0.433	3	2.29	1.31	9.94e-8	23

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Increases U7 snRNA levels but not histone 3'-end pre-mRNA processing activity, when overexpressed. Required for cell cycle progression from G1 to S phases. Binds specifically to U7 snRNA. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner. {ECO:0000269|PubMed:16914750}.;
Pathway: Gene expression (Transcription);RNA Polymerase II Transcription;SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs;Metabolism of RNA;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;SLBP independent Processing of Histone Pre-mRNAs (Consensus)

Recessive Scores

pRec: 0.105

Intolerance Scores

loftool: 0.178
rvis_EVS: -0.03
rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

pHI: 0.133
hipred: Y
hipred_score: 0.744
ghis: 0.524

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lsm10
Phenotype

Gene ontology

Biological process: termination of RNA polymerase II transcription;mRNA processing;histone mRNA metabolic process;RNA splicing;positive regulation of G1/S transition of mitotic cell cycle
Cellular component: nucleus;nucleoplasm;U7 snRNP;Cajal body;nuclear body
Molecular function: protein binding;histone pre-mRNA DCP binding;U7 snRNA binding