SNURF

Summary

SNURF (SNRPN upstream open reading frame, HGNC:11171) is a protein-coding gene on chromosome 15q11.2, encoding SNRPN upstream reading frame protein (Q9Y675).

This gene is located within the Prader-Willi Syndrome critical region on chromosome 15. Transcripts produced from this gene initiate at an imprinting center and are paternally-imprinted. These transcripts may be bicistronic and also encode SNRPN (small nuclear ribonucleoprotein polypeptide N) from a downstream open reading frame. The small protein represented by this gene is encoded by an evolutionarily-conserved upstream open reading frame and is localized to the nucleus. Extensive alternative splicing and promoter usage occurs in this region and the full-length nature of some of these transcripts has not been determined. Alterations in the imprinting center are associated with parental imprint switch failure, which may cause Angelman syndrome or Prader-Willi syndrome.

Source: NCBI Gene 8926 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Dosage sensitivity (ClinGen): haploinsufficiency little evidence, triplosensitivity no evidence
• MANE Select transcript: NM_001394334

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11171
Approved symbol	SNURF
Name	SNRPN upstream open reading frame
Location	15q11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000273173
Ensembl biotype	protein_coding
Entrez	8926

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000338327, ENST00000577949, ENST00000580062

RefSeq mRNA: 3 — MANE Select: NM_001394334 NM_001394334, NM_005678, NM_022804

CCDS: CCDS10016

Canonical transcript exons

ENST00000577949 — 3 exons

Exon	Start	End
ENSE00003703991	24962114	24962209
ENSE00003978180	24967932	24968821
ENSE00003978181	24954987	24955062

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 93.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 97.1455 / max 1119.4938, expressed in 1611 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
145497	97.1455	1611
207436	0.0332	14

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	93.62	gold quality
ganglionic eminence	UBERON:0004023	92.48	gold quality
stromal cell of endometrium	CL:0002255	92.13	gold quality
adrenal tissue	UBERON:0018303	91.98	gold quality
islet of Langerhans	UBERON:0000006	91.62	gold quality
skeletal muscle tissue	UBERON:0001134	89.45	gold quality
superior frontal gyrus	UBERON:0002661	89.44	gold quality
right atrium auricular region	UBERON:0006631	89.30	gold quality
heart left ventricle	UBERON:0002084	88.58	gold quality
heart	UBERON:0000948	88.56	gold quality
corpus callosum	UBERON:0002336	87.78	gold quality
descending thoracic aorta	UBERON:0002345	87.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.79	gold quality
ascending aorta	UBERON:0001496	86.45	gold quality
thoracic aorta	UBERON:0001515	86.45	gold quality
muscle tissue	UBERON:0002385	86.40	gold quality
gastrocnemius	UBERON:0001388	85.09	gold quality
muscle of leg	UBERON:0001383	84.90	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.42	gold quality
pituitary gland	UBERON:0000007	84.38	gold quality
adenohypophysis	UBERON:0002196	84.31	gold quality
adrenal gland	UBERON:0002369	83.60	gold quality
right coronary artery	UBERON:0001625	83.59	gold quality
popliteal artery	UBERON:0002250	83.30	gold quality
hindlimb stylopod muscle	UBERON:0004252	83.29	gold quality
tibial artery	UBERON:0007610	83.27	gold quality
ventricular zone	UBERON:0003053	83.24	gold quality
gall bladder	UBERON:0002110	83.11	gold quality
left lobe of thyroid gland	UBERON:0001120	83.10	gold quality
thyroid gland	UBERON:0002046	83.08	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.58

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1, TBP, TFCP2, WT1

miRNA regulators (miRDB)

61 targeting SNURF, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-6861-3P	99.60	68.46	444
HSA-MIR-6758-3P	99.57	67.55	1078
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-6852-5P	99.17	66.69	2073

Functional genomics

ClinGen dosage: haploinsufficiency 1 (little evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 5)

• The SNURF-SNRPN sense/UBE3A antisense transcription unit spans more than 460 kb. (PMID:11726556)
• Identification of cis- and trans-acting regulatory elements within the endogenous SNURF-SNRPN locus. (PMID:16116039)
• Differences between genetic subtypes were also statistically significant in Prader Willi syndrome (PMID:21227640)
• significant IGF2 hypermethylation (20 +/- 10 vs. 14 +/- 7%; p<0.05) and SNURF hypomethylation (23 +/- 6 vs. 32 6%; p<0.001) was found in Albright’s hereditary osteodystrophy patients vs. controls. (PMID:22679513)
• A de novo 6.4 kb deletion at 15q11.2, containing exon 1 of the SNURF gene and exon 1 of the shortest isoform of the SNRPN gene was identified in a patient with Prader-Willi-like phenotype. DNA methylation analysis confirmed the paternal origin of the deletion. (PMID:28554868)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Snurf	ENSMUSG00000102627
rattus_norvegicus	Snurf-ps2	ENSRNOG00000022595
rattus_norvegicus	Snurf	ENSRNOG00000089795

Protein

Protein identifiers

SNRPN upstream reading frame protein — Q9Y675 (reviewed: Q9Y675)

All UniProt accessions (1): Q9Y675

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Expressed in heart, skeletal muscle and lymphoblasts (at protein level). Expressed in brain, pancreas, heart, liver, lung, kidney and skeletal muscle.

Miscellaneous. Encoded on a bicistronic transcript that code for two proteins, SNRPN and SNURF. In addition to the primary 1.6-kb bicistronic SNURF-SNRPN transcript, SNURF-only transcript is also detected.

Similarity. Belongs to the SNURF family.

RefSeq proteins (3): NP_001381263, NP_005669, NP_073715 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009847	SNURF	Family

Pfam: PF07192

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y675-F1	52.06	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 43 (showing top): GCACCTT_MIR18A_MIR18B, TGCGCANK_UNKNOWN, YY1_Q6, chr15q11, MUELLER_PLURINET, AFFAR_YY1_TARGETS_UP, MODULE_48, MODULE_95, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOMF_ATPASE_BINDING, COLINA_TARGETS_OF_4EBP1_AND_4EBP2, TERAO_AOX4_TARGETS_SKIN_DN

GO Biological Process (0):

GO Molecular Function (1): ATPase binding (GO:0051117)

GO Cellular Component (2): nucleus (GO:0005634), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
enzyme binding	1
intracellular membrane-bounded organelle	1
nuclear ribonucleoprotein granule	1

Protein interactions and networks

STRING

154 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNURF	SNRPN	P14648	832
SNURF	MKRN3	Q13064	817
SNURF	NPAP1	Q9NZP6	647
SNURF	UBE3A	P78355	616
SNURF	MAGEL2	Q9UJ55	603
SNURF	NDN	Q99608	592
SNURF	PEG3	P78418	588
SNURF	ZFP57	Q9NU63	389
SNURF	DIPK1B	Q5VUD6	370
SNURF	TCEA2	Q15560	354
SNURF	UBE3B	Q7Z3V4	338
SNURF	UBE3C	Q15386	325
SNURF	SNRPB	P14678	322
SNURF	KCNN4	O15554	318
SNURF	KLHL35	Q6PF15	295

IntAct

10 interactions, top by confidence:

A	B	Type	Score
SNURF	DAPK1	psi-mi:“MI:0407”(direct interaction)	0.440
SNURF	SRPK2	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
UBE2D1	SNURF	psi-mi:“MI:0915”(physical association)	0.370
SNURF	UBE2D2	psi-mi:“MI:0915”(physical association)	0.370
SNURF	UBE2D3	psi-mi:“MI:0915”(physical association)	0.370
SNURF	UBE2D4	psi-mi:“MI:0915”(physical association)	0.370
SNURF	UBE2L6	psi-mi:“MI:0915”(physical association)	0.370
UBE2T	SNURF	psi-mi:“MI:0915”(physical association)	0.370
UBE2W	SNURF	psi-mi:“MI:0915”(physical association)	0.370
SNURF	FXR1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (7): SNURF (Affinity Capture-MS), SNURF (Affinity Capture-MS), SNURF (Reconstituted Complex), SNURF (Two-hybrid), SNURF (Affinity Capture-RNA), APP (Reconstituted Complex), SNURF (Biochemical Activity)

ESM2 similar proteins: A0A1B0GVM6, A3RLR1, A5A6K1, A6NHN6, C6Y4B0, C9J3V5, E9PJ23, E9PQR5, F5HAE6, F8W1W9, O75200, P09697, P09698, P0C5A6, P0C751, P0DTD3, P11641, P12064, P15481, P22440, P25221, P27982, P31628, P60096, P60097, P76323, P93291, Q3I5I5, Q497P3, Q5R8D4, Q5RGS7, Q6GZN9, Q6ZVQ6, Q75JF2, Q7TLC7, Q7Z2R9, Q82634, Q86SG4, Q8N976, Q8NC38

Diamond homologs: A5A6K1, B1AK76, Q9WU11, Q9WU12, Q9XS96, Q9XS97, Q9Y675

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 10 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Antigen processing: Ubiquitination & Proteasome degradation	6	22.3×	1e-06

GO biological processes:

GO term	Partners	Fold	FDR
protein K48-linked ubiquitination	5	84.3×	7e-08
protein polyubiquitination	6	69.2×	6e-09
ubiquitin-dependent protein catabolic process	5	37.1×	2e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000016488 (15:24978204 C>T), RS1000039655 (15:24971956 A>G), RS1000414212 (15:24973010 C>A), RS1000427536 (15:24960993 C>G), RS1000460176 (15:24960635 A>G), RS1000660887 (15:24955839 G>A), RS1000802119 (15:24979154 A>G), RS1001153052 (15:24963765 G>A), RS1001412574 (15:24969163 C>T), RS1001422157 (15:24976718 A>C,T), RS1001424475 (15:24977246 A>C,G), RS1001484984 (15:24965148 C>G), RS1001657010 (15:24959968 G>A), RS1001668774 (15:24955287 G>A), RS1001705908 (15:24965856 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009525_4	Panic disorder	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, increases expression, affects cotreatment	3
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
beta-methylcholine	affects expression	1
CGP 52608	affects binding, increases reaction	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
jinfukang	increases expression	1
Caffeine	decreases phosphorylation	1
Catechin	affects cotreatment, increases expression	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	increases methylation	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.