SNRNP70

protein-coding

small nuclear ribonucleoprotein U1 subunit 70, the group of RNA binding motif containing|U1 small nuclear ribonucleoprotein

Gene summary

Enables U1 snRNA binding activity. Involved in several processes, including negative regulation of chaperone-mediated autophagy; negative regulation of protein refolding; and regulation of RNA splicing. Located in lysosomal lumen and nucleoplasm. Part of U1 snRNP and spliceosomal complex. Implicated in disease of mental health and systemic lupus erythematosus. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

RNPU1Z
RPU1
SNRP70

MANE transcript

NM_003089.6

Inheritance

—

ClinVar variants

U:52B:1

Top phenotype

Global developmental delay

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr19:49,085,419-49,108,605

External References & Databases

Ensembl (ENSG00000104852)

Transcript & Mutation Effects

hg38 • Region Span ~23.2 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 SNRNP70 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 1

Global developmental delayTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003089.6. 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				1 clinvar		1
missense			47 clinvar			47
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	52	1	0	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 75 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003089.6	RefSeq	NP_003080.2	9	MANE Select
ENST00000598441.6	Ensembl	ENSP00000472998.1	9	MANE Select
NM_001301069.2	RefSeq	NP_001287998.1	9	Standard
ENST00000221448.10	Ensembl	ENSP00000221448.5	9	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
snrnp70	Danio rerio	Structure: motor neuron Quality: truncated abnormal

Gene / Model

Organism

Observed Phenotype

snrnp70

Danio rerio

Structure: motor neuron

Quality: truncated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
mRNA Processing
spliceosomal assembly
Metabolism of RNA
TCR

Biological Process

mRNA splicing, via spliceosome
regulation of ATPase activity
regulation of RNA splicing
positive regulation of mRNA splicing, via spliceosome
negative regulation of protein refolding

Molecular Function

RNA binding
mRNA binding
protein binding
U1 snRNA binding

Cellular Component

nucleus
nucleoplasm
spliceosomal complex
U1 snRNP
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000598441
Coding exons: 9
Length: 23187
Individuals with no LoFs: 114584
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 114585
p: 0.00000436

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.45	137	307	0.446	0.0000242	2753
Missense (PolyPhen)		16	89.045	0.17968		846
Synonymous	-0.956	129	116	1.11	0.00000799	898
Loss of Function	4.47	1	25.2	0.0396	0.00000200	225

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000075	0.000075	rare
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	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome. SNRNP70 binds to the loop I region of U1-snRNA. The truncated isoforms cannot bind U1-snRNA.;

Recessive Scores

pRec: 0.250

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.830

Gene Damage Prediction

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