RP9

RP9 pre-mRNA splicing factor

Basic information

Region (hg38): 7:33094797-33109405

Links

ENSG00000164610 ∙ NCBI:6100 ∙ OMIM:607331 ∙ HGNC:10288 ∙ Uniprot:Q8TA86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 9	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	8513323; 12032732

ClinVar

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

• not_provided (108 variants)
• not_specified (33 variants)
• Retinal_dystrophy (12 variants)
• Retinitis_pigmentosa_9 (8 variants)
• Retinitis_pigmentosa (8 variants)
• RP9-related_disorder (2 variants)
• Optic_atrophy (1 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. These statistics are base on transcript: NM_000203288.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	20	2	24
missense			71	2	4	77
nonsense		1	7			8
start loss			1			1
frameshift		1	6	1		8
splice donor/acceptor (+/-2bp)			2			2
Total	0	2	89	23	6

Highest pathogenic variant AF is 0.000013632978

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RP9	protein_coding	protein_coding	ENST00000297157	6	14605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0190	0.963	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.695	84	104	0.808	0.00000541	1434
Missense in Polyphen		15	23.113	0.64899		313
Synonymous	0.849	30	36.5	0.821	0.00000200	382
Loss of Function	2.07	5	13.1	0.382	8.43e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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

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

Mouse Genome Informatics

• Gene name: Rp9

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