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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	57096
Gene name Gene Name - the full gene name approved by the HGNC.	RPGR interacting protein 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	RPGRIP1
Synonyms (NCBI Gene) Gene synonyms aliases	CORD13, LCA6, RGI1, RGRIP, RPGRIP, RPGRIP1d
Chromosome Chromosome number	14
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	14q11.2
Summary Summary of gene provided in NCBI Entrez Gene.	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

Protein

UniProt ID

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

Show/Hide Causal Diseases (6)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Cone Dystrophy	cone dystrophy	rs1883036406	N/A
Cone-rod dystrophy	cone-rod dystrophy 13	rs1429786931, rs192003551, rs759940113, rs61751266, rs376500610, rs752175052, rs535922252, rs863224913, rs780667159, rs1064797182, rs771116776, rs28937883, rs745741473, rs776289402, rs752263228 View all (4 more)	N/A
cone-rod dystrophy	Cone-rod dystrophy	rs1420750126	N/A
Leber Congenital Amaurosis	Leber congenital amaurosis 6, leber congenital amaurosis, Leber congenital amaurosis 1	rs886039911, rs1594180177, rs759940113, rs1555302710, rs61751266, rs376500610, rs1429786931, rs786205623, rs1057518122, rs780667159, rs752175052, rs535922252, rs776698746, rs192003551, rs1566674809 View all (29 more)	N/A
retinal dystrophy	Retinal dystrophy	rs1883031542, rs535922252, rs1739469293, rs376500610, rs878853392, rs776289402, rs745741473, rs878853391, rs28937883, rs752263228, rs878853390, rs1594280740, rs1882854195, rs577932201, rs1420750126 View all (3 more)	N/A
Retinitis Pigmentosa	retinitis pigmentosa	rs1371805993, rs1594224781, rs1594280914, rs1555302710, rs1594214013	N/A

Show/Hide Unknown Diseases (5)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Anophthalmia/Microphthalmia-Esophageal Atresia Syndrome	Anophthalmia-microphthalmia syndrome	N/A	N/A	ClinVar
Joubert Syndrome	joubert syndrome 7	N/A	N/A	ClinVar
Microcephaly	microcephaly	N/A	N/A	ClinVar
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
Strabismus	Strabismus	N/A	N/A	GWAS

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text Mining Disease 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)