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

ENSG00000105618NCBI:26121OMIM:606419HGNC:15446Uniprot:Q8WWY3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Retinitis pigmentosa 11ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic5764686; 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 (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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
113
clinvar
9
clinvar
132
missense
2
clinvar
14
clinvar
185
clinvar
2
clinvar
203
nonsense
36
clinvar
18
clinvar
54
start loss
3
2
5
frameshift
75
clinvar
49
clinvar
2
clinvar
126
splice donor/acceptor (+/-2bp)
34
clinvar
29
clinvar
1
clinvar
64
Total 150 112 198 115 9

Highest pathogenic variant AF is 0.0000247906

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PRPF31protein_codingprotein_codingENST00000321030 1316304
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9830.0169125703011257040.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.051643170.5180.00002313227
Missense in Polyphen58133.090.435781221
Synonymous-0.4021431371.040.0000112971
Loss of Function4.14325.60.1170.00000121312

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008800.00000880
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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