SNRPN

small nuclear ribonucleoprotein polypeptide N, the group of Sm spliceosomal proteins

Basic information

Region (hg38): 15:24823637-24978723

Previous symbols: [ "PWCR" ]

Links

ENSG00000128739 ∙ NCBI:6638 ∙ OMIM:182279 ∙ HGNC:11164 ∙ Uniprot:P63162 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Prader-Willi syndrome (Definitive), mode of inheritance: AD

ClinVar

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

• not_provided (32 variants)
• not_specified (21 variants)
• Autism_spectrum_disorder (10 variants)
• Prader-Willi_syndrome (2 variants)
• Autism (1 variants)
• Angelman_syndrome (1 variants)
• SNRPN-related_condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRPN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003097.6. 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				8	3	11
missense			34			34
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	8	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRPN	protein_coding	protein_coding	ENST00000400100	7	155077

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0432	0.932	125678	0	4	125682	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	66	150	0.441	0.00000823	1511
Missense in Polyphen		15	35.517	0.42233		444
Synonymous	-0.252	52	49.7	1.05	0.00000264	542
Loss of Function	1.95	4	11.0	0.365	6.28e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.0000556	0.0000544
South Asian	0.0000365	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in tissue-specific alternative RNA processing events.
• Pathway: Prader-Willi and Angelman Syndrome;mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.400

Intolerance Scores

• loftool: 0.163
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.698
• hipred: Y
• hipred_score: 0.631
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrpn
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA splicing;response to hormone
• Cellular component: nucleoplasm;spliceosomal complex;U5 snRNP;U1 snRNP;U2 snRNP;U4 snRNP;cytoplasm;small nuclear ribonucleoprotein complex;U4/U6 x U5 tri-snRNP complex;U2-type prespliceosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding