SNUPN

snurportin 1

Basic information

Region (hg38): 15:75598083-75626469

Previous symbols: [ "RNUT1" ]

Links

ENSG00000169371 ∙ NCBI:10073 ∙ OMIM:607902 ∙ HGNC:14245 ∙ Uniprot:O95149 ∙ 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 SNUPN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNUPN 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in SNUPN

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

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

Position	Type	Phenotype	Significance	ClinVar
15-75598453-C-T		not specified	Uncertain significance (Sep 20, 2024)
15-75598465-G-A		not specified	Uncertain significance (Mar 25, 2024)
15-75598497-C-T		not specified	Uncertain significance (Sep 06, 2022)
15-75598548-T-C		not specified	Uncertain significance (Sep 04, 2024)
15-75598617-C-A		not specified	Uncertain significance (Nov 15, 2023)
15-75601196-T-A		not specified	Uncertain significance (Jan 23, 2024)
15-75601214-T-C		not specified	Uncertain significance (Jul 22, 2024)
15-75607230-A-G		not specified	Uncertain significance (Dec 18, 2023)
15-75607241-C-T		not specified	Uncertain significance (Oct 20, 2024)
15-75607249-C-T		not specified	Uncertain significance (Sep 03, 2024)
15-75607263-C-T		not specified	Uncertain significance (Jul 14, 2024)
15-75607272-T-A		not specified	Uncertain significance (Apr 20, 2024)
15-75609575-C-T		not specified	Uncertain significance (Feb 03, 2022)
15-75609641-C-T		not specified	Uncertain significance (Oct 02, 2023)
15-75609931-C-T		not specified	Uncertain significance (Dec 04, 2024)
15-75609967-C-T		not specified	Uncertain significance (Aug 05, 2024)
15-75617482-C-T		not specified	Uncertain significance (Jan 29, 2024)
15-75617547-C-T		not specified • SNUPN deficiency muscular dystrophy	Conflicting classifications of pathogenicity (Jul 03, 2024)
15-75620924-C-T		not specified	Uncertain significance (Feb 17, 2024)
15-75620925-G-A		not specified	Uncertain significance (Dec 18, 2023)
15-75620981-G-A		not specified	Uncertain significance (Jul 30, 2024)
15-75621033-C-A		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNUPN	protein_coding	protein_coding	ENST00000564644	8	28387

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.11e-14	0.0112	125659	0	88	125747	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.608	175	199	0.879	0.0000104	2368
Missense in Polyphen		54	56.579	0.95442		634
Synonymous	1.09	63	75.0	0.840	0.00000393	661
Loss of Function	-0.157	21	20.2	1.04	0.00000110	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000530	0.000530
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000433	0.000431
Middle Eastern	0.000273	0.000272
South Asian	0.000556	0.000555
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs. {ECO:0000269|PubMed:10209022, ECO:0000269|PubMed:15920472, ECO:0000269|PubMed:16030253, ECO:0000269|PubMed:9670026}.
• Pathway: RNA transport - Homo sapiens (human);snRNP Assembly;Metabolism of RNA;Metabolism of non-coding RNA (Consensus)

Intolerance Scores

• loftool: 0.518
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.0938
• hipred: Y
• hipred_score: 0.515
• ghis: 0.485

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snupn

Gene ontology

• Biological process: spliceosomal snRNP assembly;protein import into nucleus;import into nucleus;snRNA import into nucleus
• Cellular component: nuclear pore;cytosol
• Molecular function: RNA cap binding;protein binding;nuclear import signal receptor activity