SNRNP48

small nuclear ribonucleoprotein U11/U12 subunit 48, the group of U11/U12 di-snRNP|U11 small nuclear ribonucleoprotein

Basic information

Region (hg38): 6:7590197-7611967

Previous symbols: [ "C6orf151" ]

Links

ENSG00000168566 ∙ NCBI:154007 ∙ ∙ HGNC:21368 ∙ Uniprot:Q6IEG0 ∙ 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 SNRNP48 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRNP48 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in SNRNP48

This is a list of pathogenic ClinVar variants found in the SNRNP48 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-7590269-G-C		not specified	Uncertain significance (Jul 25, 2023)
6-7590269-G-T		not specified	Uncertain significance (Jun 23, 2023)
6-7590297-C-A		not specified	Uncertain significance (Aug 20, 2023)
6-7590339-A-G		not specified	Uncertain significance (Dec 02, 2022)
6-7593738-A-G		not specified	Uncertain significance (Oct 06, 2021)
6-7593746-A-G		not specified	Uncertain significance (Jan 06, 2023)
6-7593749-T-C		not specified	Uncertain significance (Jul 09, 2021)
6-7593827-G-T		not specified	Uncertain significance (Feb 22, 2023)
6-7594107-G-T		not specified	Uncertain significance (Feb 02, 2024)
6-7594157-T-C		not specified	Uncertain significance (Jan 11, 2023)
6-7601345-C-A		not specified	Uncertain significance (Feb 16, 2023)
6-7601431-G-A		not specified	Uncertain significance (Jun 05, 2023)
6-7601444-C-G		not specified	Uncertain significance (Jan 19, 2024)
6-7605402-T-C		not specified	Uncertain significance (May 24, 2024)
6-7605405-G-A		not specified	Uncertain significance (Dec 17, 2023)
6-7605432-A-T		not specified	Uncertain significance (Feb 16, 2023)
6-7605465-A-G		not specified	Uncertain significance (Oct 10, 2023)
6-7606096-A-G		not specified	Uncertain significance (Feb 13, 2023)
6-7606105-G-A		not specified	Uncertain significance (May 30, 2023)
6-7606113-A-G		not specified	Uncertain significance (Oct 30, 2023)
6-7606161-G-T		not specified	Uncertain significance (Apr 28, 2022)
6-7608827-A-T		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRNP48	protein_coding	protein_coding	ENST00000342415	9	21769

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.57e-9	0.467	125712	0	22	125734	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	114	163	0.697	0.00000840	2209
Missense in Polyphen		17	38.279	0.44411		526
Synonymous	0.668	50	56.4	0.887	0.00000273	583
Loss of Function	0.987	15	19.7	0.760	0.00000123	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000223	0.000214
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000998	0.0000967
Middle Eastern	0.000110	0.000109
South Asian	0.000150	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Likely involved in U12-type 5' splice site recognition. {ECO:0000269|PubMed:19217400}.
• Pathway: Metabolism of RNA;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

• loftool: 0.883
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.333
• ghis: 0.571

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrnp48

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleoplasm;U12-type spliceosomal complex;cytosol
• Molecular function: metal ion binding