LSM10

protein-coding

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

Gene summary

Enables U7 snRNA binding activity. Involved in positive regulation of G1/S transition of mitotic cell cycle. Located in Cajal body. Part of U7 snRNP. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_032881.3

Inheritance

—

ClinVar variants

U:17

Top phenotype

Fraser syndrome 3

gnomAD constraint

pLI —, LoF o/e 1.31

Max pathogenic AF

—

Genomic locus

chr1:36,391,238-36,397,908

External References & Databases

Ensembl (ENSG00000181817)

Transcript & Mutation Effects

hg38 • Region Span ~6.7 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 LSM10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 16

Fraser syndrome 3Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032881.3. 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						0
missense			17 clinvar			17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	17	0	0	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032881.3	RefSeq	NP_116270.1	1	MANE Select
ENST00000315732.3	Ensembl	ENSP00000319341.2	1	MANE Select
ENST00000861455.1	Ensembl	ENSP00000531514.1	1	Standard
ENST00000861456.1	Ensembl	ENSP00000531515.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

protein binding
histone pre-mRNA DCP binding
U7 snRNA binding

Cellular Component

nucleus
nucleoplasm
U7 snRNP
Cajal body
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000315732
Coding exons: 1
Length: 6655
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125744
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.468	72	84.1	0.856	0.00000626	801
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.178
RVIS EVS: -0.03
RVIS percentile EVS: 51.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.876

Gene Damage Prediction

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