RP9

RP9 pre-mRNA splicing factor

Basic information

Region (hg38): 7:33094796-33109405

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 (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	2	13
missense			42		2	44
nonsense			4			4
start loss			1			1
frameshift			3			3
inframe indel			2			2
splice donor/acceptor (+/-2bp)			2			2
splice region			3	5		8
non coding			2	11	4	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)
7-33094917-C-T		Retinitis pigmentosa	Likely benign (Jan 12, 2018)
7-33095152-T-A		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
7-33095159-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
7-33095235-CA-C		not specified • Retinitis Pigmentosa, Dominant • Retinitis pigmentosa 9	Benign/Likely benign (Apr 01, 2024)
7-33095251-C-G		not specified	Uncertain significance (Oct 13, 2023)
7-33095265-G-A		Retinal dystrophy	Benign (Oct 01, 2023)
7-33095268-G-C		Retinitis pigmentosa • not specified	Conflicting classifications of pathogenicity (Dec 07, 2021)
7-33095271-T-C		not specified • Retinitis pigmentosa • Retinitis pigmentosa 9	Benign (Nov 07, 2023)
7-33095280-C-T		Retinal dystrophy	Benign (Oct 01, 2023)
7-33095283-T-G		not specified	Uncertain significance (Nov 03, 2022)
7-33095288-C-T		RP9-related disorder	Likely benign (Jun 01, 2022)
7-33095292-T-A			Uncertain significance (Jul 14, 2017)
7-33095292-TTTTTC-T		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
7-33095316-T-A		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
7-33095364-G-A		not specified	Uncertain significance (Sep 17, 2021)
7-33095371-T-C		not specified	Uncertain significance (Mar 24, 2023)
7-33095391-T-C		Retinitis pigmentosa 9 • Retinitis pigmentosa	Uncertain significance (Apr 27, 2017)
7-33095414-C-T			Likely benign (May 01, 2022)
7-33095427-T-C		not specified	Uncertain significance (Apr 20, 2023)
7-33095430-A-G		not specified	Uncertain significance (Nov 29, 2023)
7-33096473-T-C			Likely benign (May 16, 2023)
7-33096473-TATC-T			Likely benign (Sep 12, 2022)
7-33096479-C-A			Likely benign (Jan 12, 2024)
7-33096481-GGAC-G			Likely benign (Jun 05, 2022)

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