SNRNP200

small nuclear ribonucleoprotein U5 subunit 200, the group of Spliceosomal Bact complex|Spliceosomal P complex|Spliceosomal C complex|U5 small nuclear ribonucleoprotein|RNA helicases

Basic information

Region (hg38): 2:96274338-96321271

Previous symbols: [ "ASCC3L1", "RP33" ]

Links

ENSG00000144028 ∙ NCBI:23020 ∙ OMIM:601664 ∙ HGNC:30859 ∙ Uniprot:O75643 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa 33 (Definitive), mode of inheritance: AD
• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis pigmentosa 33 (Strong), mode of inheritance: AD
• retinitis pigmentosa 33 (Definitive), mode of inheritance: AD
• SNRNP200-related dominant retinopathy (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 33	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	16612614; 19878916; 21618346; 23029027

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNRNP200 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRNP200 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			14	296	13	323
missense	1	9	404	22	4	440
nonsense			4			4
start loss			1			1
frameshift		2	3			5
inframe indel			8			8
splice donor/acceptor (+/-2bp)			6			6
splice region			50	67	3	120
non coding			19	168	13	200
Total	1	11	459	486	30

Variants in SNRNP200

This is a list of pathogenic ClinVar variants found in the SNRNP200 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-96274513-G-GAT		Retinitis Pigmentosa, Dominant	Likely benign (Jun 14, 2016)
2-96274675-C-T		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-96274679-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-96274681-C-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-96274725-G-C		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-96274755-G-C		Retinitis pigmentosa	Benign (Jan 13, 2018)
2-96274803-A-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-96274911-T-C		Retinitis pigmentosa	Likely benign (Jan 13, 2018)
2-96274912-G-A		Retinitis pigmentosa	Likely benign (Jan 13, 2018)
2-96274951-A-G		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-96274975-T-C		Retinitis pigmentosa	Likely benign (Jan 12, 2018)
2-96275013-C-G			Uncertain significance (Sep 01, 2022)
2-96275015-A-G			Likely benign (Aug 02, 2023)
2-96275026-T-C			Uncertain significance (Jan 03, 2022)
2-96275034-T-C			Uncertain significance (Jun 13, 2020)
2-96275036-A-G			Likely benign (Jul 23, 2022)
2-96275039-T-C			Likely benign (Oct 12, 2021)
2-96275054-G-A		Retinitis pigmentosa	Conflicting classifications of pathogenicity (Jan 26, 2024)
2-96275090-G-A			Likely benign (Aug 17, 2023)
2-96275109-G-A		Inborn genetic diseases	Uncertain significance (Jun 27, 2022)
2-96275114-G-A			Likely benign (Nov 03, 2023)
2-96275115-T-C		Autosomal dominant retinitis pigmentosa	Uncertain significance (May 07, 2022)
2-96275128-T-C			Uncertain significance (Dec 14, 2023)
2-96275131-C-T			Uncertain significance (Jan 19, 2024)
2-96275132-T-C		Retinitis pigmentosa • Retinal dystrophy	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRNP200	protein_coding	protein_coding	ENST00000323853	45	31224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.46e-16	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.94	610	1.19e+3	0.515	0.0000774	14073
Missense in Polyphen		168	472.67	0.35543		5603
Synonymous	0.769	436	457	0.954	0.0000282	4148
Loss of Function	9.44	4	112	0.0358	0.00000703	1269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes. Involved in spliceosome assembly, activation and disassembly. Mediates changes in the dynamic network of RNA-RNA interactions in the spliceosome. Catalyzes the ATP-dependent unwinding of U4/U6 RNA duplices, an essential step in the assembly of a catalytically active spliceosome. {ECO:0000269|PubMed:16723661, ECO:0000269|PubMed:23045696, ECO:0000269|PubMed:8670905, ECO:0000269|PubMed:9539711}.
• Disease: DISEASE: Retinitis pigmentosa 33 (RP33) [MIM:610359]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:16723661, ECO:0000269|PubMed:19710410, ECO:0000269|PubMed:19878916, ECO:0000269|PubMed:21618346, ECO:0000269|PubMed:23029027, ECO:0000269|PubMed:23045696, ECO:0000269|PubMed:23887765, ECO:0000269|PubMed:24319334}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.112
• rvis_EVS: -2.34
• rvis_percentile_EVS: 1.17

Haploinsufficiency Scores

• pHI: 0.370
• hipred: Y
• hipred_score: 0.783
• ghis: 0.650

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrnp200
• Phenotype: limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: snrnp200
• Affected structure: retinal rod cell
• Phenotype tag: abnormal
• Phenotype quality: physical object quality

Gene ontology

• Biological process: cis assembly of pre-catalytic spliceosome;spliceosome conformational change to release U4 (or U4atac) and U1 (or U11);mRNA splicing, via spliceosome;osteoblast differentiation
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U5 snRNP;membrane;U4/U6 x U5 tri-snRNP complex;catalytic step 2 spliceosome;post-mRNA release spliceosomal complex
• Molecular function: RNA binding;ATP-dependent RNA helicase activity;protein binding;ATP binding;ATP-dependent helicase activity;identical protein binding