PRPF31

pre-mRNA processing factor 31, the group of U4/U6 small nuclear ribonucleoprotein

Basic information

Region (hg38): 19:54115409-54131719

Previous symbols: [ "RP11" ]

Links

ENSG00000105618 ∙ NCBI:26121 ∙ OMIM:606419 ∙ HGNC:15446 ∙ Uniprot:Q8WWY3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa 11 (Definitive), mode of inheritance: AD
• retinitis pigmentosa 11 (Strong), mode of inheritance: AD
• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis pigmentosa 11 (Definitive), mode of inheritance: AD
• PRPF31-related retinopathy (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 11	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	5764686; 9345108; 11545739; 12923864; 17325180; 19506198; 19618371; 20939871; 23041261

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRPF31 gene.

• not provided (459 variants)
• Retinitis pigmentosa (93 variants)
• Retinal dystrophy (50 variants)
• Retinitis pigmentosa 11 (44 variants)
• Inborn genetic diseases (11 variants)
• not specified (3 variants)
• Retinitis Pigmentosa, Dominant (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF31 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			6	71	11	88
missense		2	130			132
nonsense	27	7				34
start loss	1	1				2
frameshift	54	25	1			80
inframe indel			4			4
splice donor/acceptor (+/-2bp)	27	22				49
splice region	1	1	18	15	3	38
non coding	1		15	53	14	83
Total	110	57	156	124	25

Highest pathogenic variant AF is 0.0000289

Variants in PRPF31

This is a list of pathogenic ClinVar variants found in the PRPF31 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54115463-C-T		Retinitis Pigmentosa, Dominant	Likely benign (Jun 14, 2016)
19-54115599-G-A		Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)
19-54115619-C-A		Retinitis Pigmentosa, Dominant	Conflicting classifications of pathogenicity (Dec 01, 2022)
19-54115679-G-A		Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)
19-54115693-G-C		Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)
19-54115774-A-C		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
19-54115785-G-T		Retinitis pigmentosa	Likely benign (Jan 12, 2018)
19-54115798-G-A		Retinitis pigmentosa 11	Likely pathogenic (Jun 21, 2021)
19-54115798-G-T		Retinitis pigmentosa	Likely pathogenic (Feb 06, 2024)
19-54115800-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
19-54115811-G-G		Retinitis pigmentosa	Benign (Jan 13, 2018)
19-54118273-C-A		Retinal dystrophy	Uncertain significance (Oct 10, 2017)
19-54118279-A-T		Retinitis pigmentosa	Likely pathogenic (Jan 01, 2015)
19-54118280-T-A			Pathogenic (Oct 17, 2023)
19-54118281-G-A		Retinitis pigmentosa	Likely pathogenic (May 28, 2019)
19-54118281-G-C			Pathogenic (Dec 03, 2022)
19-54118281-GTC-G			Pathogenic (Sep 12, 2022)
19-54118283-C-G			Uncertain significance (Dec 22, 2021)
19-54118300-T-C			Likely benign (Feb 18, 2023)
19-54118301-T-G			Pathogenic (Dec 03, 2021)
19-54118311-C-G			Likely benign (Jun 01, 2022)
19-54118311-C-T		Retinitis pigmentosa	Uncertain significance (Apr 27, 2017)
19-54118320-A-C			Likely benign (Jul 21, 2022)
19-54118323-A-C			Likely benign (May 12, 2022)
19-54118330-G-T			Pathogenic (Oct 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF31	protein_coding	protein_coding	ENST00000321030	13	16304

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0169	125703	0	1	125704	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.05	164	317	0.518	0.0000231	3227
Missense in Polyphen		58	133.09	0.43578		1221
Synonymous	-0.402	143	137	1.04	0.0000112	971
Loss of Function	4.14	3	25.6	0.117	0.00000121	312

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)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11867543, PubMed:28781166). Required for the assembly of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome (PubMed:11867543). {ECO:0000269|PubMed:11867543, ECO:0000269|PubMed:28781166}.
• Disease: DISEASE: Retinitis pigmentosa 11 (RP11) [MIM:600138]: 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:11545739, ECO:0000269|PubMed:12444105, ECO:0000269|PubMed:12923864, ECO:0000269|PubMed:17412961, ECO:0000269|PubMed:8808602}. 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;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.315

Intolerance Scores

• loftool: 0.170
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.05

Haploinsufficiency Scores

• pHI: 0.222
• hipred: Y
• hipred_score: 0.831
• ghis: 0.573

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpf31
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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: prpf31
• Affected structure: photoreceptor cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: spliceosomal tri-snRNP complex assembly;mRNA splicing, via spliceosome;snoRNA localization;ribonucleoprotein complex localization
• Cellular component: nucleus;nucleoplasm;U2-type spliceosomal complex;U4 snRNP;U4atac snRNP;Cajal body;nuclear speck;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome;MLL1 complex
• Molecular function: RNA binding;protein binding;U4 snRNA binding;U4atac snRNA binding;ribonucleoprotein complex binding;snRNP binding