PRPF3

pre-mRNA processing factor 3, the group of U4/U6 small nuclear ribonucleoprotein

Basic information

Region (hg38): 1:150321479-150353233

Previous symbols: [ "RP18" ]

Links

ENSG00000117360 ∙ NCBI:9129 ∙ OMIM:607301 ∙ HGNC:17348 ∙ Uniprot:O43395 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa 18 (Moderate), mode of inheritance: AD
• retinitis pigmentosa 18 (Strong), mode of inheritance: AD
• retinitis pigmentosa (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 18	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	11773002

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRPF3 gene.

• not provided (4 variants)
• Retinitis pigmentosa 18 (3 variants)
• Retinitis pigmentosa (2 variants)
• Retinal dystrophy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF3 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			4	78	4	86
missense	4	3	129	5	1	142
nonsense	1				1	2
start loss						0
frameshift			1			1
inframe indel			3			3
splice donor/acceptor (+/-2bp)	1	2	2		1	6
splice region			8	16		24
non coding			11	46	30	87
Total	6	5	150	129	37

Variants in PRPF3

This is a list of pathogenic ClinVar variants found in the PRPF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-150321489-T-TGGC		Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)
1-150321502-G-A		Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)
1-150321508-A-G		Retinitis Pigmentosa, Dominant	Likely benign (Jun 14, 2016)
1-150321523-T-C		Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)
1-150321561-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
1-150324779-C-A			Benign (May 15, 2021)
1-150324787-T-C			Benign (May 15, 2021)
1-150324880-C-CTTT			Benign (Jun 02, 2021)
1-150324893-A-T		Retinitis pigmentosa 18	Uncertain significance (May 28, 2019)
1-150324953-C-T			Uncertain significance (Aug 04, 2023)
1-150324985-A-G			Uncertain significance (Jul 04, 2024)
1-150324987-A-C			Likely benign (Aug 17, 2024)
1-150324990-G-A			Likely benign (Mar 26, 2021)
1-150325029-G-A			Likely benign (May 02, 2024)
1-150325044-A-T			Likely benign (Jul 12, 2022)
1-150325050-C-T			Likely benign (Jul 19, 2022)
1-150325057-G-A			Uncertain significance (Sep 11, 2024)
1-150325065-C-T			Likely benign (Aug 30, 2023)
1-150325069-G-A			Uncertain significance (Dec 05, 2022)
1-150325070-A-G		Inborn genetic diseases	Uncertain significance (Apr 22, 2024)
1-150325086-C-T			Likely benign (Oct 28, 2024)
1-150325091-T-A			Uncertain significance (Jan 16, 2022)
1-150325093-T-C			Uncertain significance (Oct 25, 2024)
1-150325096-CT-C			Likely benign (Jul 01, 2022)
1-150325557-C-T			Benign (May 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF3	protein_coding	protein_coding	ENST00000324862	15	31747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.47e-7	125676	0	1	125677	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.85	160	368	0.435	0.0000203	4477
Missense in Polyphen		30	112.35	0.26703		1376
Synonymous	0.573	122	130	0.936	0.00000667	1330
Loss of Function	6.12	0	43.6	0.00	0.00000324	431

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
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	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). {ECO:0000269|PubMed:26912367, ECO:0000269|PubMed:28781166, ECO:0000305|PubMed:20595234}.
• Disease: DISEASE: Retinitis pigmentosa 18 (RP18) [MIM:601414]: 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:11773002, ECO:0000269|PubMed:12714658, ECO:0000269|PubMed:17932117}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.0311
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.831
• hipred: Y
• hipred_score: 0.833
• ghis: 0.580

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpf3
• 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); vision/eye phenotype; pigmentation phenotype

Zebrafish Information Network

• Gene name: prpf3
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: spliceosomal tri-snRNP complex assembly;RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;mRNA processing;RNA splicing
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;cytosol;Cajal body;nuclear speck;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome
• Molecular function: RNA binding;protein binding;identical protein binding