SNURF

SNRPN upstream open reading frame

Basic information

Region (hg38): 15:24954986-24977850

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.

• Autism spectrum disorder (7 variants)
• Inborn genetic diseases (5 variants)
• not provided (1 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	9	0	0

Variants in SNURF

This is a list of pathogenic ClinVar variants found in the SNURF region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-24962118-C-T		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24962124-C-T		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24962126-C-T		Autism spectrum disorder	Conflicting classifications of pathogenicity (Dec 31, 2019)
15-24962151-G-A		not specified	Uncertain significance (Aug 30, 2022)
15-24962217-C-G		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24967946-C-T		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24967950-G-C		not specified	Uncertain significance (Aug 11, 2021)
15-24967951-C-T		not specified	Uncertain significance (Jan 03, 2022)
15-24967952-G-A		Autism spectrum disorder • not specified	Uncertain significance (Feb 28, 2023)
15-24967964-A-G		not specified	Uncertain significance (Sep 15, 2021)
15-24967964-A-T		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24967975-G-A		not specified	Uncertain significance (Oct 14, 2023)
15-24968030-G-A		not specified	Uncertain significance (Jul 12, 2022)
15-24974305-C-T		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24974344-T-G		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24974365-T-C		Autism spectrum disorder	Benign/Likely benign (Jun 19, 2021)
15-24974368-G-A		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24974415-G-A		Autism spectrum disorder	Likely benign (Jun 14, 2016)
15-24974434-G-T		Autism spectrum disorder	Uncertain significance (Jun 14, 2016)
15-24974462-C-G		not specified	Uncertain significance (Mar 11, 2024)
15-24974466-A-G		Autism spectrum disorder	Conflicting classifications of pathogenicity (Dec 31, 2019)
15-24975420-A-C			Uncertain significance (Jun 09, 2022)
15-24976317-G-A			Likely benign (Aug 15, 2018)
15-24976331-G-A			Uncertain significance (Dec 23, 2020)
15-24976332-T-C		Autism spectrum disorder	Conflicting classifications of pathogenicity (Apr 06, 2018)

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