SNRPB2

small nuclear ribonucleoprotein polypeptide B2, the group of RNA binding motif containing|U2 small nuclear ribonucleoprotein

Basic information

Region (hg38): 20:16729961-16742564

Links

ENSG00000125870 ∙ NCBI:6629 ∙ OMIM:603520 ∙ HGNC:11155 ∙ Uniprot:P08579 ∙ 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 SNRPB2 gene.

• not_specified (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRPB2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003092.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			16			16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRPB2	protein_coding	protein_coding	ENST00000246071	6	11816

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0506	0.930	125730	0	15	125745	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	64	118	0.542	0.00000558	1490
Missense in Polyphen		10	32.216	0.31041		451
Synonymous	-0.147	41	39.8	1.03	0.00000189	404
Loss of Function	2.03	4	11.4	0.351	5.53e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000963	0.0000963
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000742	0.0000703
Middle Eastern	0.000110	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346). Associated with sn-RNP U2, where it contributes to the binding of stem loop IV of U2 snRNA (PubMed:9716128). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:28781166, ECO:0000269|PubMed:9716128}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;spliceosomal assembly;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.712
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.371
• hipred: Y
• hipred_score: 0.807
• ghis: 0.689

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.924

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrpb2

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: fibrillar center;nucleus;nucleoplasm;spliceosomal complex;U1 snRNP;U2 snRNP;nuclear speck;U2-type precatalytic spliceosome;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
• Molecular function: protein binding;U1 snRNA binding;snRNA stem-loop binding;snRNP binding