Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	57096
Gene name	RPGR interacting protein 1
Gene symbol	RPGRIP1
Synonyms (NCBI Gene)	CORD13LCA6RGI1RGRIPRPGRIPRPGRIP1d
Chromosome	14
Chromosome location	14q11.2
Summary	This gene encodes a photoreceptor protein that interacts with retinitis pigmentosa GTPase regulator protein and is a key component of cone and rod photoreceptor cells. Mutations in this gene lead to autosomal recessive congenital blindness. [provided by R

Show/Hide all (67)

SNP ID	Visualize variation	Clinical significance	Consequence
rs10151259	G>T	Likely-benign, benign, pathogenic, not-provided	Coding sequence variant, missense variant
rs17103671	A>G	Likely-benign, pathogenic, benign-likely-benign, benign	Coding sequence variant, missense variant
rs28937883	G>A,T	Not-provided, pathogenic	Intron variant, coding sequence variant, missense variant
rs61751266	A>-	Not-provided, pathogenic	Genic upstream transcript variant, coding sequence variant, frameshift variant
rs61751270	->T	Pathogenic	Coding sequence variant, frameshift variant
rs75459701	C>T	Pathogenic, uncertain-significance	Intron variant, coding sequence variant, stop gained
rs137853124	G>A	Pathogenic	Stop gained, genic upstream transcript variant, coding sequence variant
rs140904308	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, genic upstream transcript variant
rs147586703	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, intron variant
rs150107283	A>G	Conflicting-interpretations-of-pathogenicity, likely-benign	Genic upstream transcript variant, intron variant
rs190490019	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, missense variant
rs192003551	C>A,T	Pathogenic	Genic upstream transcript variant, coding sequence variant, synonymous variant, stop gained
rs199590641	C>T	Conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, missense variant
rs200510462	T>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic upstream transcript variant, coding sequence variant, missense variant
rs201384449	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic upstream transcript variant, coding sequence variant, missense variant
rs372615343	A>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance	Genic upstream transcript variant, coding sequence variant, missense variant
rs374188857	A>G	Likely-pathogenic	Genic upstream transcript variant, splice acceptor variant
rs376500610	G>A	Pathogenic, likely-pathogenic	Genic upstream transcript variant, splice donor variant
rs398124354	G>A	Pathogenic	Coding sequence variant, stop gained
rs535922252	A>G,T	Pathogenic	Coding sequence variant, intron variant, missense variant
rs554396590	C>T	Pathogenic	Genic upstream transcript variant, stop gained, coding sequence variant
rs565837539	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant, intron variant
rs574462207	A>G	Pathogenic	Coding sequence variant, synonymous variant, genic upstream transcript variant
rs577932201	C>G,T	Likely-pathogenic	Coding sequence variant, missense variant, stop gained, intron variant
rs587783012	CGAAGGC>-	Pathogenic	Coding sequence variant, frameshift variant
rs587783018	C>A,T	Pathogenic	Coding sequence variant, synonymous variant, genic upstream transcript variant, stop gained
rs587783019	C>T	Pathogenic	Coding sequence variant, stop gained, intron variant
rs751342895	A>G	Pathogenic	Splice acceptor variant, genic upstream transcript variant, upstream transcript variant
rs751521888	A>G,T	Likely-pathogenic	Intron variant, missense variant, coding sequence variant
rs752175052	C>T	Pathogenic	Stop gained, coding sequence variant
rs752263228	C>-	Likely-pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant
rs758239674	G>A	Likely-pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant
rs759940113	C>A,T	Pathogenic	Stop gained, intron variant, synonymous variant, coding sequence variant
rs771116776	G>A,T	Pathogenic	Splice donor variant
rs775935766	C>T	Likely-pathogenic, uncertain-significance	Intron variant, stop gained, coding sequence variant
rs776289402	->T	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs776698746	->CT	Pathogenic	Frameshift variant, coding sequence variant
rs776880045	A>-	Likely-pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant
rs780587095	C>G,T	Pathogenic	Intron variant, stop gained, coding sequence variant, missense variant
rs780667159	C>T	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs781728563	G>-	Likely-pathogenic	Intron variant
rs786205623	A>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs863224913	G>-	Likely-pathogenic	Coding sequence variant, splice acceptor variant
rs878853389	->A	Likely-pathogenic	Intron variant, frameshift variant, coding sequence variant
rs878853390	T>-	Likely-pathogenic	Intron variant, frameshift variant, coding sequence variant
rs878853391	T>A	Likely-pathogenic	Coding sequence variant, 5 prime UTR variant, stop gained, genic upstream transcript variant, upstream transcript variant
rs878853392	A>T	Likely-pathogenic	Coding sequence variant, stop gained, genic upstream transcript variant
rs886039911	AGAGGTGAGTTGCCATCATCA>-	Likely-pathogenic	Coding sequence variant, intron variant, splice donor variant, genic upstream transcript variant
rs1057518122	G>A	Likely-pathogenic, pathogenic	Intron variant
rs1064797181	G>A	Uncertain-significance, pathogenic	Upstream transcript variant, synonymous variant, coding sequence variant, genic upstream transcript variant
rs1064797182	A>G	Likely-pathogenic	Intron variant, splice acceptor variant
rs1325103400	G>A	Pathogenic	Splice donor variant
rs1371805993	C>T	Pathogenic	Stop gained, coding sequence variant
rs1420750126	GAACTGGAGG>-	Pathogenic	5 prime UTR variant, frameshift variant, coding sequence variant
rs1429786931	C>T	Pathogenic	Intron variant, coding sequence variant, stop gained
rs1555302200	->TT	Likely-pathogenic	Coding sequence variant, intron variant, frameshift variant
rs1555302710	T>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555303320	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1566341956	C>T	Pathogenic	Stop gained, coding sequence variant, intron variant
rs1566674809	AATAATTTAGCGCCTTTCTCTGCAGAGCTTCCATTAAAGAGAAGGTAGAGCTGATTCGACTTAAGAAG>-	Pathogenic	Genic upstream transcript variant, splice acceptor variant, coding sequence variant, intron variant
rs1594180177	GA>-	Pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1594202505	G>C	Pathogenic	Upstream transcript variant, intron variant, genic upstream transcript variant
rs1594203796	G>A	Likely-pathogenic	5 prime UTR variant, intron variant
rs1594214013	A>G	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs1594224781	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs1594280740	GTTTA>-	Pathogenic	Splice acceptor variant, intron variant, coding sequence variant
rs1594280914	AGAA>-	Pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (2)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029762	hsa-miR-26b-5p	Microarray	19088304
MIRT1315621	hsa-miR-584	CLIP-seq

Show/Hide all (23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	16339905, 21224891, 25398945, 25416956, 25910212, 26638075, 26871637, 27173435, 31515488
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IDA
GO:0005929	Component	Cilium	IEA
GO:0005930	Component	Axoneme	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	IEA
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0032391	Component	Photoreceptor connecting cilium	IBA
GO:0032391	Component	Photoreceptor connecting cilium	IEA
GO:0032391	Component	Photoreceptor connecting cilium	ISS
GO:0042462	Process	Eye photoreceptor cell development	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043005	Component	Neuron projection	IEA
GO:0045171	Component	Intercellular bridge	IDA
GO:0046548	Process	Retinal rod cell development	IBA
GO:0060041	Process	Retina development in camera-type eye	IEA
GO:0061351	Process	Neural precursor cell proliferation	IEA
GO:0097730	Component	Non-motile cilium	IEA
GO:0120206	Component	Photoreceptor distal connecting cilium	IEA
GO:1905515	Process	Non-motile cilium assembly	IBA

MIM	HGNC	e!Ensembl
605446	13436	ENSG00000092200

Q96KN7

Protein name

X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGR-interacting protein 1)

Protein function

May function as scaffolding protein. Required for normal location of RPGR at the connecting cilium of photoreceptor cells. Required for normal disk morphogenesis and disk organization in the outer segment of photoreceptor cells and for survival

PDB

4QAM

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF11618	C2-C2_1	618 → 757	First C2 domain of RPGR-interacting protein 1	Domain
PF00168	C2	799 → 908	C2 domain	Domain
PF18111	RPGR1_C	1114 → 1279	Retinitis pigmentosa G-protein regulator interacting C-terminal	Domain

Tissue specificity

TISSUE SPECIFICITY: Strong expression in retina, with weaker expression in testis. Expressed in other neurons such as amacrine cells. Colocalizes with RGPR in the outer segment of rod photoreceptors and cone outer segments. {ECO:0000269|PubMed:10958647, E

Sequence

MSHLVDPTSGDLPVRDIDAIPLVLPASKGKNMKTQPPLSRMNREELEDSFFRLREDHMLV
KELSWKQQDEIKRLRTTLLRLTAAGRDLRVAEEAAPLSETARRGQKAGWRQRLSMHQRPQ
MHRLQGHFHCVGPASPRRAQPRVQVGHRQLHTAGAPVPEKPKRGPRDRLSYTAPPSFKEH
ATNENRGEVASKPSELVSGSNSIISFSSVISMAKPIGLCMPNSAHIMASNTMQVEEPPKS
PEKMWPKDENFEQRSSLECAQKAAELRASIKEKVELIRLKKLLHERNASLVMTKAQLTEV
QEAYETLLQKNQGILSAAHEALLKQVNELRAELKEESKKAVSLKSQLEDVSILQMTLKEF
QERVEDLEKERKLLNDNYDKLLESMLDSSDSSSQPHWSNELIAEQLQQQVSQLQDQLDAE
LEDKRKVLLELSREKAQNEDLKLEVTNILQKHKQEVELLQNAATISQPPDRQSEPATHPA
VLQENTQIEPSEPKNQEEKKLSQVLNELQVSHAETTLELEKTRDMLILQRKINVCYQEEL
EAMMTKADNDNRDHKEKLERLTRLLDLKNNRIKQLEGILRSHDLPTSEQLKDVAYGTRPL
SLCLETLPAHGDEDKVDISLLHQGENLFELHIHQAFLTSAALAQAGDTQPTTFCTYSFYD
FETHCTPLSVGPQPLYDFTSQYVMETDSLFLHYLQEASARLDIHQAMASEHSTLAAGWIC
FDRVLETVEKVHGLATLIGAGGEEFGVLEYWMRLRFPIKPSLQACNKRKKAQVYLSTDVL
GGRKAQEEEFRSESWEPQNELWIEITKCCGLRSRWLGTQPSPYAVYRFFTFSDHDTAIIP
ASNNPYFRDQARFPVLVTSDLDHYLRREALSIHVFDDEDLEPGSYLGRARVPLLPLAKNE
SIKGDFNLTDPAEKPNGSIQVQLDWKFPYIPPESFLKPEAQTKGKDTKDSSKISSEEEKA
SFPSQDQMASPEVPIEAGQYRSKRKPPHGGERKEKEHQVVSYSRRKHGKRIGVQGKNRME
YLSLNILNGNTPEQVNYTEWKFSETNSFIGDGFKNQHEEEEMTLSHSALKQKEPLHPVND
KESSEQGSEVSEAQTTDSDDVIVPPMSQKYPKADSEKMCIEIVSLAFYPEAEVMSDENIK
QVYVEYKFYDLPLSETETPVSLRKPRAGEEIHFHFSKVIDLDPQEQQGRRRFLFDMLNGQ
DPDQGHLKFTVVSDPLDEEKKECEEVGYAYLQLWQILESGRDILEQELDIVSPEDLATPI
GRLKVSLQAAAVLHAIYKEMTEDLFS

Sequence length

1286

Interactions

View interactions

1891

Show/Hide Causal Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the eye	Pathogenic	rs565837539	RCV000504829
Color vision defect	Likely pathogenic	rs1555302200	RCV000626951
Cone dystrophy	Pathogenic	rs1883036406	RCV001199769
Cone-rod dystrophy	Likely pathogenic; Pathogenic	rs1420750126	RCV002267761
Cone-rod dystrophy 13	Pathogenic; Likely pathogenic	rs398124354, rs61751266, rs1181453325, rs2139156519, rs2139160608, rs763671264, rs771116776, rs1225223445, rs1233376985, rs2139175288, rs1881002905, rs1412625438, rs2139168888, rs1566674893, rs2139350315 View all (77 more)	RCV001800387 RCV001047199 RCV001381712 RCV001388371 RCV001381649 RCV001387658 RCV001931715 RCV001999910 RCV001863942 RCV001920939 RCV001958920 RCV001891436 RCV002007259 RCV002007139 RCV002037770 RCV001876898 RCV002018117 RCV001963002 RCV001958667 RCV001956430 RCV001871080 RCV001875567 RCV002048259 RCV001975616 RCV001948841 RCV001922256 RCV001380810 RCV003062612 RCV003079173 RCV003098964 RCV002602786 RCV000175918 RCV002635361 RCV000005274 RCV002890476 RCV002867673 RCV002933549 RCV000195884 RCV003016409 RCV003045809 RCV003044972 RCV002516255 RCV002518810 RCV005220741 RCV003781400 RCV003787544 RCV003788383 RCV003792304 RCV003806158 RCV003790886 RCV003791448 RCV003802833 RCV003795242 RCV003802722 RCV003807396 RCV001387165 RCV001800704 RCV001238890 RCV001215982 RCV001382205 RCV001238568 RCV001854022 RCV001800828 RCV002532181 RCV001201958 RCV000701424 RCV000701308 RCV000686083 RCV000762921 RCV000714541 RCV001335049 RCV001800880 RCV001228179 RCV001858702 RCV001380451 RCV001862727 RCV001385916 RCV003769397 RCV001800914 RCV001034879 RCV001062863 RCV001054263 RCV001862500 RCV001212958 RCV001237909 RCV001236080 RCV001238762 RCV001236081 RCV001238536 RCV001238537 RCV001880011 RCV001389834 RCV002537617 RCV003770355
Horizontal nystagmus	Likely pathogenic	rs1555302200	RCV000626951
Leber congenital amaurosis	Pathogenic; Likely pathogenic	rs398124354, rs61751266, rs587783012, rs137853124, rs2502980632, rs1439947338, rs1057518122, rs1064797182, rs776880045, rs565837539, rs1555302710, rs780667159, rs1555303320, rs775935766, rs751342895 View all (4 more)	RCV000710048 RCV000786015 RCV001262111 RCV000787885 RCV003123514 RCV003486516 RCV000515742 RCV001199768 RCV000504638 RCV002230986 RCV005418176 RCV000504726 RCV000504916 RCV003226328 RCV002282254 RCV000710047 RCV001844254 RCV004526076 RCV003324559
Leber congenital amaurosis 1	Pathogenic; Likely pathogenic	rs780667159, rs376500610, rs61751270	RCV000989177 RCV000989170 RCV000989176
Leber congenital amaurosis 6	Pathogenic; Likely pathogenic	rs398124354, rs2139160690, rs61751266, rs61751268, rs61751271, rs61751265, rs1181453325, rs2139156519, rs2139160608, rs763671264, rs765001696, rs771116776, rs1225223445, rs1233376985, rs2139175288 View all (104 more)	RCV001800386 RCV001376537 RCV000171128 RCV001261183 RCV002225287 RCV001261170 RCV001381712 RCV001388371 RCV001381649 RCV001387658 RCV001526702 RCV001931715 RCV001999910 RCV001863942 RCV001920939 RCV001958920 RCV001891436 RCV002007259 RCV002007139 RCV002037770 RCV001876898 RCV002018117 RCV001963002 RCV001958667 RCV001956430 RCV001871080 RCV001875567 RCV002048259 RCV001975616 RCV001948841 RCV001922256 RCV000144462 RCV000144463 RCV000144469 RCV000144470 RCV002250894 RCV003062612 RCV001261172 RCV003079173 RCV003098964 RCV002602786 RCV001261169 RCV002635361 RCV000005271 RCV002890476 RCV002867673 RCV002933549 RCV003016409 RCV003045809 RCV003044972 RCV001198056 RCV002516255 RCV000256440 RCV002518810 RCV005220741 RCV003781400 RCV003787544 RCV003788383 RCV003792304 RCV003806158 RCV003790886 RCV003791448 RCV003802833 RCV003795242 RCV003802722 RCV003807396 RCV003989944 RCV001261193 RCV001800703 RCV001238890 RCV001215982 RCV001261187 RCV001261192 RCV001238568 RCV001854022 RCV001389835 RCV000625855 RCV001261186 RCV000678628 RCV000678627 RCV000701424 RCV000701308 RCV000686083 RCV000754600 RCV000754601 RCV000714540 RCV000761349 RCV001800879 RCV001228179 RCV001858702 RCV001267701 RCV001862727 RCV001385916 RCV003769397 RCV001005012 RCV001005013 RCV001005014 RCV001005011 RCV001005021 RCV001034879 RCV001062863 RCV001054263 RCV001862500 RCV001212958 RCV001237909 RCV001236080 RCV001238762 RCV001236081 RCV001238536 RCV001238537 RCV001261176 RCV001261175 RCV001261174 RCV001261188 RCV001261171 RCV001261178 RCV001261179 RCV001261181 RCV001261182 RCV001261184 RCV001261189 RCV001261177 RCV001261190
Lung cancer	Pathogenic	rs771116776	RCV005924269
Retinal disorder	Pathogenic	rs1371805993	RCV006272304
Retinal dystrophy	Likely pathogenic; Pathogenic	rs1740380459, rs28937883, rs878853392, rs878853391, rs878853390, rs577932201, rs878853389, rs371900300, rs1429786931, rs1555302200, rs776289402, rs752263228, rs376500610, rs1420750126, rs1594280740 View all (6 more)	RCV004815592 RCV004794325 RCV000225543 RCV000225431 RCV000225615 RCV000225680 RCV000225501 RCV004818414 RCV001074918 RCV000626951 RCV001075715 RCV001074662 RCV004818098 RCV004818143 RCV001074771 RCV001074229 RCV001075703 RCV001074230 RCV001073673 RCV001074723 RCV001073416
Retinitis pigmentosa	Likely pathogenic; Pathogenic	rs192003551, rs1555302710, rs1594214013, rs1371805993, rs1594224781, rs1594280914	RCV005417990 RCV000505086 RCV001003209 RCV001003210 RCV001003211 RCV001003212
RPGRIP1-related disorder	Likely pathogenic; Pathogenic	rs775935766, rs75459701	RCV003420017 RCV003403585
Visual impairment	Likely pathogenic	rs1555302200	RCV000626951

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs1882924452, rs1882902603	-
Anophthalmia-microphthalmia syndrome	Conflicting classifications of pathogenicity; Likely benign	rs372615343, rs869025257	RCV000207372 RCV000207424
Bardet-Biedl syndrome	Uncertain significance	rs374913550, rs1429217156	RCV003224782 RCV003224789
Cone-Rod Dystrophy, Recessive	Conflicting classifications of pathogenicity	rs578107768	RCV000297795
Joubert syndrome 7	Uncertain significance	rs1389509266	RCV001029761
Microcephaly	Uncertain significance	rs188312873	RCV001252813
Optic atrophy	Conflicting classifications of pathogenicity	rs181758389	RCV004815014
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs188660364	RCV005913730

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Cone Rod Dystrophies	Associate	23776498, 28456785
Glaucoma	Associate	21224891
Glaucoma Open Angle	Associate	21224891, 34427245
Leber Congenital Amaurosis	Associate	11283794, 15024725, 18682808, 18936139, 19753312, 21602930, 24066033, 25775262, 27880076, 28456785, 28966547, 29193763, 29844330, 31087526, 32736544 View all (6 more)
Low Tension Glaucoma	Associate	21224891
Macular Degeneration	Associate	33907365
Nystagmus Pathologic	Associate	11283794
Refsum Disease Infantile	Associate	33907365
Retinal Degeneration	Associate	30072743, 31087526, 33907365
Retinal Diseases	Associate	25775262
Retinal Dystrophies	Associate	24625443, 25943428, 27391102, 34427245, 37761981
Retinitis Pigmentosa	Associate	16272259, 28456785, 29193763, 30543658, 33907365, 40296824

RPGRIP1 (RPGR interacting protein 1)