SNRNP25

small nuclear ribonucleoprotein U11/U12 subunit 25, the group of U11/U12 di-snRNP|U11 small nuclear ribonucleoprotein

Basic information

Region (hg38): 16:53827-57669

Previous symbols: [ "C16orf33" ]

Links

ENSG00000161981 ∙ NCBI:79622 ∙ ∙ HGNC:14161 ∙ Uniprot:Q9BV90 ∙ 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 SNRNP25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRNP25 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						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in SNRNP25

This is a list of pathogenic ClinVar variants found in the SNRNP25 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-55466-T-C		not specified	Uncertain significance (Jul 19, 2022)
16-55514-C-T		not specified	Uncertain significance (Oct 22, 2021)
16-55528-A-G		not specified	Uncertain significance (Feb 23, 2023)
16-55779-G-A		not specified	Uncertain significance (Aug 19, 2023)
16-56546-G-C		not specified	Uncertain significance (Aug 02, 2021)
16-56559-A-G		not specified	Uncertain significance (Aug 10, 2021)
16-56589-C-T		not specified	Uncertain significance (Oct 29, 2021)
16-56596-C-G		not specified	Uncertain significance (Oct 29, 2021)
16-57097-G-A		not specified	Uncertain significance (May 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRNP25	protein_coding	protein_coding	ENST00000383018	5	4660

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00134	0.873	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.422	70	80.7	0.868	0.00000493	848
Missense in Polyphen		19	23.283	0.81604		254
Synonymous	-0.441	36	32.8	1.10	0.00000219	251
Loss of Function	1.33	6	10.7	0.562	6.42e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.000381	0.000381
South Asian	0.000197	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of RNA;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0902

Intolerance Scores

• loftool: 0.558
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.322
• ghis: 0.581

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.691

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrnp25

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleus;nucleoplasm;U12-type spliceosomal complex;cytosol;intercellular bridge
• Molecular function: protein binding