SNRNP70

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

Basic information

Region (hg38): 19:49085418-49108605

Previous symbols: [ "RNPU1Z", "RPU1", "SNRP70" ]

Links

ENSG00000104852 ∙ NCBI:6625 ∙ OMIM:180740 ∙ HGNC:11150 ∙ Uniprot:P08621 ∙ 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 SNRNP70 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRNP70 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in SNRNP70

This is a list of pathogenic ClinVar variants found in the SNRNP70 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-49086528-T-C			Likely benign (Jul 01, 2022)
19-49098448-A-G		not specified	Uncertain significance (Nov 17, 2022)
19-49107815-C-T		not specified	Uncertain significance (Nov 12, 2021)
19-49107901-C-T		Global developmental delay	Uncertain significance (Jan 01, 2020)
19-49107907-C-G		not specified	Uncertain significance (Mar 13, 2023)
19-49107998-G-T		not specified	Uncertain significance (Jan 24, 2024)
19-49108063-G-A		not specified	Uncertain significance (Mar 29, 2022)
19-49108064-G-T		not specified	Uncertain significance (Jan 09, 2024)
19-49108109-C-G		not specified	Uncertain significance (May 02, 2023)
19-49108114-G-C		not specified	Uncertain significance (Jun 06, 2023)
19-49108114-G-T		not specified	Uncertain significance (Nov 10, 2022)
19-49108124-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-49108219-C-T		not specified	Uncertain significance (Aug 03, 2022)
19-49108256-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-49108292-G-T		not specified	Uncertain significance (Dec 05, 2022)
19-49108309-G-C		not specified	Uncertain significance (Dec 20, 2023)
19-49108325-A-C		not specified	Uncertain significance (Jun 29, 2022)
19-49108360-C-G		not specified	Uncertain significance (Nov 08, 2022)
19-49108372-A-G		not specified	Uncertain significance (Apr 27, 2023)
19-49108382-A-C		not specified	Uncertain significance (Jan 10, 2023)
19-49108393-G-A		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRNP70	protein_coding	protein_coding	ENST00000598441	9	23187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000743	114584	0	1	114585	0.00000436

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.45	137	307	0.446	0.0000242	2753
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000753	0.0000753
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;spliceosomal assembly;Metabolism of RNA;TCR;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.250

Haploinsufficiency Scores

• pHI: 0.548
• hipred: Y
• hipred_score: 0.840
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.830

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrnp70

Zebrafish Information Network

• Gene name: snrnp70
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: truncated

Gene ontology

• 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;negative regulation of chaperone-mediated autophagy
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U1 snRNP;nuclear speck
• Molecular function: RNA binding;mRNA binding;protein binding;U1 snRNA binding