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GeneBe

RP9

RP9 pre-mRNA splicing factor

Basic information

Region (hg38): 7:33094796-33109405

Links

ENSG00000164610NCBI:6100OMIM:607331HGNC:10288Uniprot:Q8TA86AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • retinitis pigmentosa (Supportive), mode of inheritance: AD
  • retinitis pigmentosa 9 (Strong), mode of inheritance: AD
  • retinitis pigmentosa 9 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Retinitis pigmentosa 9ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic8513323; 12032732

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RP9 gene.

  • not provided (78 variants)
  • Retinitis pigmentosa (14 variants)
  • Inborn genetic diseases (14 variants)
  • Retinitis pigmentosa 9 (6 variants)
  • not specified (5 variants)
  • Retinitis Pigmentosa, Dominant (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RP9 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
11
clinvar
2
clinvar
13
missense
42
clinvar
2
clinvar
44
nonsense
4
clinvar
4
start loss
1
clinvar
1
frameshift
3
clinvar
3
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
?
3
5
8
non coding
?
2
clinvar
11
clinvar
4
clinvar
17
Total 0 0 56 22 8

Variants in RP9

This is a list of pathogenic ClinVar variants found in the RP9 region.

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

Position Type Phenotype Significance ClinVar
7-33094814-G-C Retinitis pigmentosa Benign (Jan 13, 2018)360043
7-33094917-C-T Retinitis pigmentosa Likely benign (Jan 12, 2018)909960
7-33095152-T-A Retinitis pigmentosa Uncertain significance (Jan 12, 2018)910856
7-33095159-G-A Retinitis pigmentosa Uncertain significance (Jan 13, 2018)360044
7-33095235-CA-C not specified • Retinitis Pigmentosa, Dominant • Retinitis pigmentosa 9 Benign/Likely benign (Nov 01, 2023)198295
7-33095268-G-C Retinitis pigmentosa • Inborn genetic diseases Conflicting classifications of pathogenicity (Dec 07, 2021)795939
7-33095271-T-C not specified • Retinitis pigmentosa • Retinitis pigmentosa 9 Benign (Nov 07, 2021)167609
7-33095283-T-G Inborn genetic diseases Uncertain significance (Nov 03, 2022)2322285
7-33095292-T-A Uncertain significance (Jul 14, 2017)450590
7-33095316-T-A Retinitis pigmentosa Uncertain significance (Jan 12, 2018)910857
7-33095364-G-A Inborn genetic diseases Uncertain significance (Sep 17, 2021)2251213
7-33095371-T-C Inborn genetic diseases Uncertain significance (Mar 24, 2023)2529709
7-33095391-T-C Retinitis pigmentosa 9 • Retinitis pigmentosa Uncertain significance (Apr 27, 2017)3335
7-33095414-C-T Likely benign (May 01, 2022)2657382
7-33095427-T-C Inborn genetic diseases Uncertain significance (Apr 20, 2023)2539607
7-33096473-TATC-T Likely benign (Sep 12, 2022)1977882
7-33096479-C-A Likely benign (Apr 21, 2022)1940715
7-33096481-GGAC-G Likely benign (Jun 05, 2022)2002491
7-33096484-C-T Likely benign (Feb 03, 2022)1899551
7-33096485-G-A Likely benign (Dec 09, 2022)2050907
7-33096485-G-T Likely benign (Aug 15, 2022)1957787
7-33096497-C-T not specified • Retinitis pigmentosa Benign (Oct 20, 2022)167610
7-33096498-G-A Likely benign (Oct 27, 2021)1534495
7-33096501-C-T not specified • Retinitis pigmentosa Benign (Jan 12, 2024)167611
7-33096504-T-C Likely benign (Dec 15, 2021)1945022

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RP9protein_codingprotein_codingENST00000297157 614605
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01900.9631257350131257480.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.695841040.8080.000005411434
Missense in Polyphen1523.1130.64899313
Synonymous0.8493036.50.8210.00000200382
Loss of Function2.07513.10.3828.43e-7145

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0001850.000185
European (Non-Finnish)0.00006160.0000615
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Is thought to be a target protein for the PIM1 kinase. May play some roles in B-cell proliferation in association with PIM1 (By similarity). {ECO:0000250}.;
Pathway
Spliceosome - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.195

Intolerance Scores

loftool
0.624
rvis_EVS
0.17
rvis_percentile_EVS
65.33

Haploinsufficiency Scores

pHI
0.127
hipred
Y
hipred_score
0.526
ghis
0.508

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.903

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rp9
Phenotype

Gene ontology

Biological process
RNA splicing;cognition
Cellular component
nucleus;signal recognition particle receptor complex;cytosol
Molecular function
RNA binding;protein binding;metal ion binding