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.

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.

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			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	5	0	0

Variants in SNRPB2

This is a list of pathogenic ClinVar variants found in the SNRPB2 region.

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

Position	Phenotype	Significance	ClinVar
20-16732245-G-T	not specified	Uncertain significance (Dec 20, 2023)	3167050
20-16732278-G-A	not specified	Uncertain significance (Dec 28, 2022)	2340046
20-16732326-G-A	not specified	Uncertain significance (Jul 09, 2021)	2203826
20-16737384-A-G	not specified	Uncertain significance (Jun 29, 2023)	2608856
20-16740347-A-G	not specified	Uncertain significance (Apr 11, 2023)	2560918
20-16740846-G-A	not specified	Likely benign (Jan 09, 2024)	3167051

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
Phenotype

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