SNRPB

small nuclear ribonucleoprotein polypeptides B and B1, the group of Sm spliceosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 20:2461634-2470853

Previous symbols: [ "SNRPB1" ]

Links

ENSG00000125835 ∙ NCBI:6628 ∙ OMIM:182282 ∙ HGNC:11153 ∙ Uniprot:P14678 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cerebrocostomandibular syndrome (Strong), mode of inheritance: AD
• cerebrocostomandibular syndrome (Supportive), mode of inheritance: AD
• cerebrocostomandibular syndrome (Moderate), mode of inheritance: Semidominant

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cerebrocostomandibular syndrome	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	25047197; 25504470; 26971886

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNRPB gene.

• SNRPB-related disorder (1 variants)
• Cerebro-costo-mandibular syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRPB 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				24	3	27
missense		1	36	1	1	39
nonsense						0
start loss						0
frameshift		1	2			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1	3	7	1	12
non coding	1			14	9	24
Total	1	2	38	39	13

Variants in SNRPB

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

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

Position	Type	Phenotype	Significance	ClinVar
20-2461767-G-A			Uncertain significance (Dec 22, 2021)
20-2461772-C-T			Likely benign (Jun 15, 2023)
20-2461773-G-A			Uncertain significance (Feb 05, 2021)
20-2461777-T-TC			Uncertain significance (Sep 26, 2022)
20-2461780-C-T			Benign (Dec 10, 2023)
20-2461781-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jul 09, 2023)
20-2461781-G-C			Uncertain significance (Jan 19, 2024)
20-2461785-G-A			Uncertain significance (Aug 19, 2022)
20-2461785-G-T		Inborn genetic diseases	Uncertain significance (Jan 12, 2024)
20-2461790-G-A		not specified	Uncertain significance (Sep 11, 2017)
20-2461792-C-A		SNRPB-related disorder	Uncertain significance (Sep 12, 2024)
20-2462470-G-A			Benign (May 16, 2021)
20-2462619-C-T			Likely benign (Dec 11, 2023)
20-2462632-T-C			Uncertain significance (Dec 30, 2022)
20-2462667-C-T			Likely benign (Dec 16, 2023)
20-2462668-G-A			Uncertain significance (Jan 13, 2022)
20-2462670-A-G			Likely benign (Aug 27, 2023)
20-2462699-CA-C			Likely pathogenic (Nov 29, 2022)
20-2462705-G-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
20-2462706-G-C			Uncertain significance (Dec 15, 2023)
20-2462709-C-T		SNRPB-related disorder	Benign (Jan 26, 2024)
20-2462714-T-A			Uncertain significance (Apr 17, 2022)
20-2462714-T-C			Uncertain significance (Jul 12, 2016)
20-2462717-G-A			Benign (Jan 19, 2024)
20-2462749-G-T			Uncertain significance (Dec 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRPB	protein_coding	protein_coding	ENST00000438552	7	9220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.709	0.291	123389	0	2	123391	0.00000810

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	85	149	0.569	0.00000813	1522
Missense in Polyphen		8	33.465	0.23906		420
Synonymous	-0.184	53	51.3	1.03	0.00000294	531
Loss of Function	2.79	2	12.8	0.157	8.54e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000181
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. As part of the U7 snRNP it is involved in histone 3'-end processing. {ECO:0000269|PubMed:18984161}.
• Disease: DISEASE: Cerebrocostomandibular syndrome (CCMS) [MIM:117650]: A syndrome characterized by severe micrognathia, rib defects ranging from a few dorsal rib segments to complete absence of ossification, and mental retardation. {ECO:0000269|PubMed:25047197, ECO:0000269|PubMed:25504470}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Systemic lupus erythematosus - Homo sapiens (human);Spliceosome - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);snRNP Assembly;RNA Polymerase II Transcription;SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs;Metabolism of RNA;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Metabolism of non-coding RNA;SLBP independent Processing of Histone Pre-mRNAs;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.443
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.658
• hipred: Y
• hipred_score: 0.701
• ghis: 0.689

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrpb

Gene ontology

• Biological process: spliceosomal snRNP assembly;mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;protein methylation;histone mRNA metabolic process;RNA splicing;import into nucleus
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U5 snRNP;U7 snRNP;U1 snRNP;U2 snRNP;U4 snRNP;U12-type spliceosomal complex;telomerase holoenzyme complex;cytoplasm;cytosol;small nuclear ribonucleoprotein complex;methylosome;SMN-Sm protein complex;U4/U6 x U5 tri-snRNP complex;U2-type prespliceosome;U2-type precatalytic spliceosome;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;histone pre-mRNA 3'end processing complex
• Molecular function: RNA binding;protein binding;telomerase RNA binding;histone pre-mRNA DCP binding