U2SURP

U2 snRNP associated SURP domain containing, the group of Spliceosomal A complex|RNA binding motif containing

Basic information

Region (hg38): 3:142964497-143060725

Links

ENSG00000163714 ∙ NCBI:23350 ∙ OMIM:617849 ∙ HGNC:30855 ∙ Uniprot:O15042 ∙ 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 U2SURP gene.

• not_specified (50 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the U2SURP gene is commonly pathogenic or not. These statistics are base on transcript: NM_001080415.2. 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					1	1
missense			50			50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	0	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
U2SURP	protein_coding	protein_coding	ENST00000473835	28	96229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.06e-9	123962	0	2	123964	0.00000807

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.09	245	503	0.487	0.0000261	6758
Missense in Polyphen		19	136.63	0.13906		1810
Synonymous	-0.473	175	167	1.05	0.00000863	1818
Loss of Function	7.13	1	61.2	0.0163	0.00000357	825

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000221	0.000200
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

• rvis_EVS: -0.91
• rvis_percentile_EVS: 9.9

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.725
• ghis: 0.732

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: U2surp

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA binding;protein binding