PRPF31
pre-mRNA processing factor 31, the group of U4/U6 small nuclear ribonucleoprotein
Basic information
Region (hg38): 19:54115410-54131719
Previous symbols: [ "RP11" ]
Links
Phenotypes
GenCC
Source:
- 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:
| 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
- not_provided (548 variants)
- Retinal_dystrophy (135 variants)
- Retinitis_pigmentosa (94 variants)
- Retinitis_pigmentosa_11 (74 variants)
- Inborn_genetic_diseases (32 variants)
- PRPF31-related_disorder (22 variants)
- not_specified (2 variants)
- Leber_congenital_amaurosis (1 variants)
- Cone-rod_dystrophy (1 variants)
- Early-onset_retinitis_pigmentosa (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. These statistics are base on transcript: NM_000015629.4. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | 113 | 132 | |||
| missense | 14 | 185 | 203 | |||
| nonsense | 36 | 18 | 54 | |||
| start loss | 3 | 2 | 5 | |||
| frameshift | 75 | 49 | 126 | |||
| splice donor/acceptor (+/-2bp) | 34 | 29 | 64 | |||
| Total | 150 | 112 | 198 | 115 | 9 |
Highest pathogenic variant AF is 0.0000247906
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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