GeneBe

PRPF6

protein-coding

pre-mRNA processing factor 6, the group of U5 small nuclear ribonucleoprotein

Gene summary

The protein encoded by this gene appears to be involved in pre-mRNA splicing, possibly acting as a bridging factor between U5 and U4/U6 snRNPs in formation of the spliceosome. The encoded protein also can bind androgen receptor, providing a link between transcriptional activation and splicing. [provided by RefSeq, Jul 2008]

Previous symbols:
  • C20orf14

MANE transcript

NM_012469.4

Inheritance

AD

ClinVar variants

P:5U:309B:239

Top phenotype

Retinitis pigmentosa 60

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr20:63,981,132-64,033,100

External References & Databases

Ensembl (ENSG00000101161)NCBI Gene (24148)OMIM (613979)HGNC:15860GenCCUniProt (O94906)AlphaFoldClinVar (PRPF6)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~52.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosa 60LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0013516

Submitter: G2P

retinitis pigmentosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Orphanet

retinitis pigmentosa 60MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0013516

Submitter: PanelApp Australia

retinitis pigmentosa 60LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0013516

Submitter: Ambry Genetics

retinitis pigmentosa 60STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013516

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Retinitis pigmentosa 60AD

Manifestation: Ophthalmologic

Intervention: General

Rationale: 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

Refs: 21549338Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRPF6 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 679
not specifiedTotal: 245
Retinitis pigmentosaTotal: 49
Retinal dystrophyTotal: 34
PRPF6-related disorderTotal: 28
Retinitis pigmentosa 60Total: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012469.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
7
clinvar
217
clinvar
8
clinvar
 232
missense
4
clinvar
271
clinvar
11
clinvar
 286
nonsense
1
clinvar
7
clinvar
 8
start loss
0
frameshift
14
clinvar
1
clinvar
 15
splice donor/acceptor (+/-2bp)
10
clinvar
2
clinvar
 12
Total053092318553

Highest pathogenic variant AF is 0.000010260662

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_012469.4RefSeqNP_036601.221MANE Select
ENST00000266079.5EnsemblENSP00000266079.421MANE Select
ENST00000855537.1EnsemblENSP00000525596.121Standard
ENST00000855537.2EnsemblENSP00000525596.121Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Spliceosome - Homo sapiens (human)
  • mRNA Processing
  • Metabolism of RNA
  • mRNA Splicing - Major Pathway
  • mRNA Splicing - Minor Pathway

Biological Process

  • spliceosomal tri-snRNP complex assembly
  • spliceosomal complex assembly
  • RNA splicing, via transesterification reactions
  • mRNA splicing, via spliceosome
  • RNA localization

Molecular Function

  • transcription coactivator activity
  • RNA binding
  • protein binding
  • ribonucleoprotein complex binding
  • androgen receptor binding

Cellular Component

  • nucleus
  • nucleoplasm
  • spliceosomal complex
  • U5 snRNP
  • membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000266079
Coding exons
21
Length
51966
Individuals with no LoFs
125712
Homozygous LoFs
0
Heterozygous LoFs
36
Defined
125748
p
0.000143
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense4.852425670.4270.00003916160
Missense (PolyPhen)28145.190.192851559
Synonymous-0.7502412271.060.00001611833
Loss of Function4.781552.30.2870.00000283575

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.000140.00014rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.000220.00022rare
Finnish0.000190.00018rare
European (Non-Finnish)0.000120.00011rare
South Asian0.000160.00016rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Involved in pre-mRNA splicing as component of the U4/U6- U5 tri-snRNP complex, one of the building blocks of the spliceosome (PubMed:28781166, PubMed:21549338). Enhances dihydrotestosterone-induced transactivation activity of AR, as well as dexamethasone-induced transactivation activity of NR3C1, but does not affect estrogen-induced transactivation. {ECO:0000269|PubMed:12039962, ECO:0000269|PubMed:21549338, ECO:0000269|PubMed:28781166}.;

Recessive Scores

pRec
0.357

Intolerance Scores

LoFtool
0.461
RVIS EVS
-1.38
RVIS percentile EVS
4.39

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.982

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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