SNRPN

protein-coding

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

Gene summary

This gene is located within the Prader-Willi Syndrome critical region on chromosome 15 and is imprinted and expressed from the paternal allele. It encodes a component of the small nuclear ribonucleoprotein complex, which functions in pre-mRNA processing and may contribute to tissue-specific alternative splicing. Alternative promoter use and alternative splicing result in a multitude of transcript variants encoding the same protein. Transcript variants that initiate at the CpG island-associated imprinting center may be bicistronic and also encode the SNRPN upstream reading frame protein (SNURF) from an upstream open reading frame. In addition, long spliced transcripts for small nucleolar RNA host gene 14 (SNHG14) may originate from the promoters at this locus and share exons with this gene. Alterations in this region are associated with parental imprint switch failure, which may cause Angelman syndrome or Prader-Willi syndrome. [provided by RefSeq, Mar 2017]

Previous symbols:

PWCR

MANE transcript

NM_003097.6

Inheritance

ClinVar variants

P:2U:43B:11

Top phenotype

Prader-Willi syndrome

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr15:24,823,637-24,978,723

External References & Databases

Ensembl (ENSG00000128739)

Transcript & Mutation Effects

hg38 • Region Span ~155.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Prader-Willi syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008300

Submitter: G2P

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SNRPN variants in ClinVar

6 Conditions Cataloged

not providedTotal: 39

not specifiedTotal: 23

Prader-Willi syndromeTotal: 3

AutismTotal: 1

Angelman syndromeTotal: 1

SNRPN-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003097.6. 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				8 clinvar	3 clinvar	11
missense			42 clinvar			42
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)	2 clinvar					2
Total	2	0	43	8	3	56

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 230 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003097.6	RefSeq	NP_003088.1	7	MANE Select
ENST00000390687.9	Ensembl	ENSP00000375105.4	7	MANE Select
NM_001349454.2	RefSeq	NP_001336383.1	7	Standard
NM_001349455.2	RefSeq	NP_001336384.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prader-Willi and Angelman Syndrome
mRNA Processing
Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing

Biological Process

mRNA splicing, via spliceosome
RNA splicing
response to hormone

Molecular Function

RNA binding
protein binding

Cellular Component

nucleoplasm
spliceosomal complex
U5 snRNP
U1 snRNP
U2 snRNP

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000400100
Coding exons: 7
Length: 155077
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125682
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.43	66	150	0.441	0.00000823	1511
Missense (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

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	0.000056	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000036	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in tissue-specific alternative RNA processing events.;

Recessive Scores

pRec: 0.400

Intolerance Scores

LoFtool: 0.163
RVIS EVS: -0.21
RVIS percentile EVS: 38.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0893

Gene Damage Prediction

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