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GeneBe

RP1

RP1 axonemal microtubule associated, the group of Doublecortin superfamily

Basic information

Region (hg38): 8:54509421-54871720

Links

ENSG00000104237NCBI:6101OMIM:603937HGNC:10263Uniprot:P56715AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • retinitis pigmentosa 1 (Definitive), mode of inheritance: AD
  • retinitis pigmentosa (Supportive), mode of inheritance: AD
  • retinitis pigmentosa 1 (Definitive), mode of inheritance: AD
  • retinitis pigmentosa 1 (Strong), mode of inheritance: AD
  • retinitis pigmentosa 1 (Strong), mode of inheritance: AR
  • RP1-related dominant retinopathy (Definitive), mode of inheritance: Semidominant
  • RP1-related recessive retinopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Retinitis pigmentosa 1, autosomal dominant; Retinitis pigmentosa 1, autosomal recessiveAD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic1783394; 10391211; 10391212; 18552984; 19933189; 20664799; 21746989; 22052604; 22317909; 22321012; 22917891; 23077400

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RP1 gene.

  • not provided (1154 variants)
  • Retinitis pigmentosa (145 variants)
  • Inborn genetic diseases (103 variants)
  • Retinitis pigmentosa 1 (83 variants)
  • Retinal dystrophy (56 variants)
  • not specified (23 variants)
  • Autosomal recessive retinitis pigmentosa (6 variants)
  • Retinitis Pigmentosa, Dominant (3 variants)
  • RP1-related condition (2 variants)
  • RP1-related retinal dystrophy (2 variants)
  • Hypertriglyceridemia 1 (1 variants)
  • Leber congenital amaurosis 1 (1 variants)
  • Leber optic atrophy (1 variants)
  • Retinal pigment epithelial atrophy;Retinal dystrophy;Visual impairment (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RP1 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
8
clinvar
202
clinvar
11
clinvar
221
missense
2
clinvar
5
clinvar
720
clinvar
18
clinvar
9
clinvar
754
nonsense
59
clinvar
20
clinvar
4
clinvar
83
start loss
0
frameshift
104
clinvar
27
clinvar
5
clinvar
136
inframe indel
9
clinvar
9
splice donor/acceptor (+/-2bp)
2
clinvar
2
clinvar
1
clinvar
5
splice region
5
4
1
10
non coding
9
clinvar
11
clinvar
2
clinvar
22
Total 167 54 756 231 22

Highest pathogenic variant AF is 0.0000460

Variants in RP1

This is a list of pathogenic ClinVar variants found in the RP1 region.

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

Position Type Phenotype Significance ClinVar
8-54616061-T-C Retinitis Pigmentosa, Dominant Likely benign (Jun 14, 2016)369611
8-54616109-G-A Retinitis pigmentosa Likely benign (Jan 13, 2018)363274
8-54616114-G-A Retinitis pigmentosa Uncertain significance (Jan 13, 2018)363275
8-54616164-A-G Retinitis pigmentosa Uncertain significance (Apr 27, 2017)912104
8-54616178-T-C Retinitis pigmentosa Uncertain significance (Apr 27, 2017)908097
8-54620943-T-C Retinitis pigmentosa Uncertain significance (Jan 13, 2018)363276
8-54620970-AGT-A Retinitis pigmentosa 1 Pathogenic (Mar 14, 2022)2500819
8-54620981-T-C Likely benign (Feb 09, 2022)2095546
8-54620987-T-C Likely benign (Oct 02, 2023)2005268
8-54620987-T-G Retinitis pigmentosa Conflicting classifications of pathogenicity (Dec 16, 2023)908098
8-54620989-G-T Inborn genetic diseases Uncertain significance (Aug 02, 2021)2241118
8-54620998-T-A Retinitis pigmentosa 1 Uncertain significance (Jan 06, 2021)1803210
8-54621001-T-C Uncertain significance (Dec 24, 2022)3006388
8-54621006-C-G Uncertain significance (Jul 05, 2023)1436527
8-54621010-C-T Uncertain significance (Oct 25, 2022)2175356
8-54621011-G-A Likely benign (Apr 15, 2023)2804516
8-54621016-C-A Uncertain significance (Aug 08, 2022)1483213
8-54621021-G-A Uncertain significance (Jan 06, 2024)2705804
8-54621025-A-C Inborn genetic diseases Uncertain significance (Jan 29, 2024)3155793
8-54621031-C-T Uncertain significance (Oct 08, 2023)848593
8-54621032-A-AC Pathogenic (Jul 13, 2022)2418953
8-54621033-C-T Uncertain significance (Aug 09, 2022)1715798
8-54621035-C-T Likely benign (Jun 24, 2023)2791725
8-54621037-C-G Uncertain significance (Aug 11, 2021)1464871
8-54621037-C-T Uncertain significance (Aug 21, 2022)1900451

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RP1protein_codingprotein_codingENST00000220676 314768
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.41e-131.0012552902191257480.000871
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.89411691.09e+31.080.000055314374
Missense in Polyphen167182.080.917162415
Synonymous0.2183903960.9860.00002104037
Loss of Function3.393057.80.5190.00000295901

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001810.00180
Ashkenazi Jewish0.000.00
East Asian0.003050.00305
Finnish0.0004630.000462
European (Non-Finnish)0.0007240.000712
Middle Eastern0.003050.00305
South Asian0.0007530.000752
Other0.001150.00114

dbNSFP

Source: dbNSFP

Function
FUNCTION: Microtubule-associated protein regulating the stability and length of the microtubule-based axoneme of photoreceptors. Required for the differentiation of photoreceptor cells, it plays a role in the organization of the outer segment of rod and cone photoreceptors ensuring the correct orientation and higher-order stacking of outer segment disks along the photoreceptor axoneme (By similarity). {ECO:0000250}.;
Disease
DISEASE: Retinitis pigmentosa 1 (RP1) [MIM:180100]: 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:10391211, ECO:0000269|PubMed:10484783, ECO:0000269|PubMed:11095597, ECO:0000269|PubMed:15863674, ECO:0000269|PubMed:15933747, ECO:0000269|PubMed:19956407, ECO:0000269|PubMed:20664799, ECO:0000269|PubMed:22052604, ECO:0000269|PubMed:22334370}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.102

Intolerance Scores

loftool
0.497
rvis_EVS
0.85
rvis_percentile_EVS
88.38

Haploinsufficiency Scores

pHI
0.338
hipred
N
hipred_score
0.203
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0265

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Rp1
Phenotype
vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Gene ontology

Biological process
visual perception;phototransduction, visible light;axoneme assembly;intracellular signal transduction;photoreceptor cell outer segment organization;photoreceptor cell development;photoreceptor cell maintenance;retinal rod cell development;retinal cone cell development;retina development in camera-type eye;cellular response to light stimulus;positive regulation of non-motile cilium assembly
Cellular component
photoreceptor outer segment;photoreceptor inner segment;microtubule;microtubule associated complex;axoneme;photoreceptor connecting cilium;ciliary tip
Molecular function
protein binding;microtubule binding