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.

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.

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					1	1
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	1

Variants in U2SURP

This is a list of pathogenic ClinVar variants found in the U2SURP region.

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

Position	Type	Phenotype	Significance	ClinVar
3-143001644-C-T		not specified	Uncertain significance (May 27, 2022)
3-143001651-G-T		not specified	Uncertain significance (Nov 08, 2024)
3-143001656-C-G		not specified	Uncertain significance (Aug 09, 2021)
3-143010858-A-G		not specified	Uncertain significance (Jun 18, 2024)
3-143012247-G-A		not specified	Uncertain significance (Oct 07, 2024)
3-143012268-G-A		not specified	Uncertain significance (Jan 29, 2024)
3-143012288-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-143016316-T-A		not specified	Uncertain significance (Apr 18, 2023)
3-143016903-T-A		not specified	Uncertain significance (Jan 02, 2024)
3-143021358-C-A		not specified	Uncertain significance (Jan 25, 2025)
3-143021490-C-T		not specified	Uncertain significance (Jan 18, 2023)
3-143022858-A-T		not specified	Uncertain significance (Jun 06, 2023)
3-143022860-G-T		not specified	Uncertain significance (Apr 11, 2023)
3-143023033-C-T		not specified	Uncertain significance (Jul 05, 2023)
3-143028488-T-G		not specified	Uncertain significance (Mar 10, 2025)
3-143028508-C-T		not specified	Uncertain significance (Jan 22, 2024)
3-143033315-A-T			Benign (Dec 31, 2019)
3-143034926-A-G		not specified	Uncertain significance (Dec 14, 2022)
3-143036007-C-T		not specified	Uncertain significance (May 24, 2023)
3-143036079-A-C		not specified	Uncertain significance (Jul 27, 2024)
3-143037270-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-143038143-A-G		not specified	Uncertain significance (Jul 06, 2024)
3-143038950-G-C		not specified	Uncertain significance (Nov 28, 2024)
3-143043207-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-143043241-A-C		not specified	Uncertain significance (Aug 08, 2023)

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