SNRPB

protein-coding

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

Gene summary

The protein encoded by this gene is one of several nuclear proteins that are found in common among U1, U2, U4/U6, and U5 small ribonucleoprotein particles (snRNPs). These snRNPs are involved in pre-mRNA splicing, and the encoded protein may also play a role in pre-mRNA splicing or snRNP structure. Autoantibodies from patients with systemic lupus erythematosus frequently recognize epitopes on the encoded protein. Two transcript variants encoding different isoforms (B and B') have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

SNRPB1

MANE transcript

NM_003091.4

Inheritance

SD, AD

ClinVar variants

P:3U:62B:38

Top phenotype

Cerebrocostomandibular syndrome

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr20:2,461,634-2,470,853

External References & Databases

Ensembl (ENSG00000125835)

Transcript & Mutation Effects

hg38 • Region Span ~9.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cerebrocostomandibular syndromeMODERATE

Inheritance Pattern: SD

Disease ID:MONDO:0007301

Submitter: Ambry Genetics

cerebrocostomandibular syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007301

Submitter: Ambry Genetics

cerebrocostomandibular syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007301

Submitter: Orphanet

cerebrocostomandibular syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007301

Submitter: G2P

cerebrocostomandibular syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007301

Submitter: Labcorp Genetics (formerly Invitae)

cerebrocostomandibular syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007301

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Cerebrocostomandibular syndromeAD

Manifestation: Craniofacial; Musculoskeletal; Neurologic

Intervention: General

Rationale: 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

Refs: 25047197; 25504470; 26971886

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SNRPB variants in ClinVar

7 Conditions Cataloged

not providedTotal: 120

Inborn genetic diseasesTotal: 15

Cerebro-costo-mandibular syndromeTotal: 7

SNRPB-related disorderTotal: 7

not specifiedTotal: 5

Isolated Pierre-Robin syndromeTotal: 1

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003091.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	35 clinvar	2 clinvar	39
missense		1 clinvar	57 clinvar		1 clinvar	59
nonsense						0
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)		1 clinvar	2 clinvar			3
Total	0	3	62	35	3	103

Highest pathogenic variant AF is 0.000005811003

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003091.4	RefSeq	NP_003082.1	7	MANE Select
ENST00000381342.7	Ensembl	ENSP00000370746.3	7	MANE Select
NM_198216.2	RefSeq	NP_937859.1	7	Standard
ENST00000438552.6	Ensembl	ENSP00000412566.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Systemic lupus erythematosus - Homo sapiens (human)
Spliceosome - Homo sapiens (human)
mRNA Processing
Gene expression (Transcription)
snRNP Assembly

Biological Process

spliceosomal snRNP assembly
mRNA splicing, via spliceosome
termination of RNA polymerase II transcription
protein methylation
histone mRNA metabolic process

Molecular Function

RNA binding
protein binding
telomerase RNA binding
histone pre-mRNA DCP binding

Cellular Component

nucleus
nucleoplasm
spliceosomal complex
U5 snRNP
U7 snRNP

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000438552
Coding exons: 7
Length: 9220
Individuals with no LoFs: 123389
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 123391
p: 0.00000810

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.87	85	149	0.569	0.00000813	1522
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.175

Intolerance Scores

LoFtool: 0.443
RVIS EVS: -0.27
RVIS percentile EVS: 33.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.973

Gene Damage Prediction

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