SNURF

SNRPN upstream open reading frame

Basic information

Region (hg38): 15:24954987-24977850

Links

ENSG00000273173 ∙ NCBI:8926 ∙ ∙ HGNC:11171 ∙ Uniprot:Q9Y675 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not_specified (12 variants)
• Autism_spectrum_disorder (7 variants)
• not_provided (2 variants)
• Prader-Willi_syndrome (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNURF gene is commonly pathogenic or not. These statistics are base on transcript: NM_001394334.1. 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				2		2
missense			13			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNURF	protein_coding	protein_coding	ENST00000338094	3	23597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.462	0.515	124683	0	2	124685	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.299	38	43.6	0.872	0.00000271	448
Missense in Polyphen		2	6.8338	0.29266		93
Synonymous	1.04	10	15.1	0.661	8.15e-7	141
Loss of Function	1.82	1	5.67	0.176	3.41e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000899	0.00000896
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Gastric Cancer Network 2;Prader-Willi and Angelman Syndrome;Metabolism of RNA;mRNA Splicing - Major Pathway;AndrogenReceptor;Coregulation of Androgen receptor activity;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

• loftool: 0.290
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.247

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.638

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snurf

Gene ontology

• Biological process: biological_process
• Cellular component: nucleus;nuclear speck
• Molecular function: molecular_function