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.	7401
Gene name Gene Name - the full gene name approved by the HGNC.	Clarin 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CLRN1
Synonyms (NCBI Gene) Gene synonyms aliases	RP61, USH3, USH3A
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3q25.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis

Show/Hide all(18)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121908140	A>C,G,T	Pathogenic	Non coding transcript variant, synonymous variant, coding sequence variant, 3 prime UTR variant, stop gained
rs121908141	A>G,T	Pathogenic	Non coding transcript variant, missense variant, synonymous variant, coding sequence variant
rs121908142	A>G	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant, 3 prime UTR variant
rs201205811	C>T	Pathogenic	Splice donor variant
rs201625237	G>A,T	Likely-pathogenic	Coding sequence variant, missense variant, 3 prime UTR variant, non coding transcript variant
rs373208120	G>A	Pathogenic	Stop gained, 3 prime UTR variant, coding sequence variant, intron variant, non coding transcript variant
rs374963432	G>T	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant
rs376155416	G>A,T	Likely-pathogenic	3 prime UTR variant, missense variant, coding sequence variant, non coding transcript variant, stop gained
rs397517932	GACAT>-	Likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs746523071	->T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, 3 prime UTR variant
rs775098953	A>C	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant, 3 prime UTR variant
rs1057516687	->A	Likely-pathogenic	Splice donor variant
rs1085307049	ATA>-	Pathogenic	3 prime UTR variant, non coding transcript variant, coding sequence variant, inframe indel
rs1231668679	A>-	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, frameshift variant, 3 prime UTR variant
rs1553772595	A>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1559982739	A>G	Pathogenic	Non coding transcript variant, missense variant, synonymous variant, coding sequence variant
rs1576623563	T>A	Likely-pathogenic	Splice acceptor variant
rs1576631624	AAGAAGGCTG>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant

Show/Hide all(58)

miRTarBase ID	miRNA	Experiments
MIRT897755	hsa-miR-30a	CLIP-seq
MIRT897756	hsa-miR-30b	CLIP-seq
MIRT897757	hsa-miR-30c	CLIP-seq
MIRT897758	hsa-miR-30d	CLIP-seq
MIRT897759	hsa-miR-30e	CLIP-seq
MIRT897760	hsa-miR-329	CLIP-seq
MIRT897761	hsa-miR-362-3p	CLIP-seq
MIRT897762	hsa-miR-3941	CLIP-seq
MIRT897763	hsa-miR-466	CLIP-seq
MIRT897764	hsa-miR-4672	CLIP-seq
MIRT897765	hsa-miR-4789-3p	CLIP-seq
MIRT897766	hsa-miR-600	CLIP-seq
MIRT897767	hsa-miR-603	CLIP-seq
MIRT897760	hsa-miR-329	CLIP-seq
MIRT897761	hsa-miR-362-3p	CLIP-seq
MIRT897762	hsa-miR-3941	CLIP-seq
MIRT897763	hsa-miR-466	CLIP-seq
MIRT897764	hsa-miR-4672	CLIP-seq
MIRT897765	hsa-miR-4789-3p	CLIP-seq
MIRT897768	hsa-miR-4802-5p	CLIP-seq
MIRT897766	hsa-miR-600	CLIP-seq
MIRT897767	hsa-miR-603	CLIP-seq
MIRT897760	hsa-miR-329	CLIP-seq
MIRT1546519	hsa-miR-3617	CLIP-seq
MIRT897761	hsa-miR-362-3p	CLIP-seq
MIRT897762	hsa-miR-3941	CLIP-seq
MIRT1546520	hsa-miR-4476	CLIP-seq
MIRT897763	hsa-miR-466	CLIP-seq
MIRT897764	hsa-miR-4672	CLIP-seq
MIRT897766	hsa-miR-600	CLIP-seq
MIRT897767	hsa-miR-603	CLIP-seq
MIRT1546521	hsa-miR-641	CLIP-seq
MIRT1546522	hsa-miR-7	CLIP-seq
MIRT1966227	hsa-miR-1185	CLIP-seq
MIRT1966228	hsa-miR-1224-5p	CLIP-seq
MIRT1966229	hsa-miR-1252	CLIP-seq
MIRT1966230	hsa-miR-214	CLIP-seq
MIRT1966231	hsa-miR-3605-5p	CLIP-seq
MIRT1966232	hsa-miR-3619-5p	CLIP-seq
MIRT1966233	hsa-miR-3679-5p	CLIP-seq
MIRT1966234	hsa-miR-3915	CLIP-seq
MIRT1966235	hsa-miR-4689	CLIP-seq
MIRT1966236	hsa-miR-4760-5p	CLIP-seq
MIRT1966237	hsa-miR-657	CLIP-seq
MIRT1966238	hsa-miR-761	CLIP-seq
MIRT2202018	hsa-miR-2277-3p	CLIP-seq
MIRT897760	hsa-miR-329	CLIP-seq
MIRT1546519	hsa-miR-3617	CLIP-seq
MIRT897761	hsa-miR-362-3p	CLIP-seq
MIRT897762	hsa-miR-3941	CLIP-seq
MIRT897763	hsa-miR-466	CLIP-seq
MIRT897764	hsa-miR-4672	CLIP-seq
MIRT897765	hsa-miR-4789-3p	CLIP-seq
MIRT2202019	hsa-miR-542-3p	CLIP-seq
MIRT897766	hsa-miR-600	CLIP-seq
MIRT897767	hsa-miR-603	CLIP-seq
MIRT1546521	hsa-miR-641	CLIP-seq
MIRT1546522	hsa-miR-7	CLIP-seq

Show/Hide all(27)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005886	Component	Plasma membrane	IDA	19423712
GO:0005886	Component	Plasma membrane	IEA
GO:0005902	Component	Microvillus	IDA	19423712
GO:0007015	Process	Actin filament organization	IDA	19423712
GO:0007601	Process	Visual perception	IEA
GO:0007605	Process	Sensory perception of sound	IBA
GO:0007605	Process	Sensory perception of sound	IEA
GO:0007605	Process	Sensory perception of sound	IEA
GO:0007605	Process	Sensory perception of sound	IMP	15650299
GO:0010592	Process	Positive regulation of lamellipodium assembly	IDA	19423712
GO:0015630	Component	Microtubule cytoskeleton	IEA
GO:0016020	Component	Membrane	IEA
GO:0030027	Component	Lamellipodium	IDA	19423712
GO:0030140	Component	Trans-Golgi network transport vesicle	IEA
GO:0032420	Component	Stereocilium	IEA
GO:0045178	Component	Basal part of cell	IEA
GO:0045494	Process	Photoreceptor cell maintenance	IMP	15521980
GO:0048870	Process	Cell motility	IDA	19423712
GO:0050885	Process	Neuromuscular process controlling balance	IEA
GO:0050885	Process	Neuromuscular process controlling balance	IEA
GO:0050953	Process	Sensory perception of light stimulus	IMP	15521980
GO:0050957	Process	Equilibrioception	IBA
GO:0050957	Process	Equilibrioception	IMP	15521980
GO:0060088	Process	Auditory receptor cell stereocilium organization	IEA
GO:0060117	Process	Auditory receptor cell development	IEA
GO:0098858	Component	Actin-based cell projection	IEA

MIM	HGNC	e!Ensembl
606397	12605	ENSG00000163646

Protein

UniProt ID

P58418

Protein name

Clarin-1 (Usher syndrome type-3 protein)

Protein function

May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.

Family and domains

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. Found in the retina.

Sequence

MPSQQKKIIFCMAGVFSFACALGVVTALGTPLWIKATVLCKTGALLVNASGQELDKFMGE
MQYGLFHGEGVRQCGLGARPFRFSFFPDLLKAIPVSIHVNVILFSAILIVLTMVGTAFFM
YNAFGKPFETLHGPLGLYLLSFISGSCGCLVMILFASEVKIHHLSEKIANYKEGTYVYKT
QSEKYTTSFWVIFFCFFVHFLNGLLIRLAGFQFPFAKSKDAETTNVAADLMY

Sequence length

232

Interactions

View interactions

Show/Hide Causal Diseases (4)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
hearing impairment	Hearing impairment	rs1553776135, rs121908140	N/A
retinal dystrophy	Retinal dystrophy	rs786204428, rs878853379, rs746523071, rs1235835151, rs1715594024, rs374390376	N/A
Retinitis Pigmentosa	retinitis pigmentosa 61, retinitis pigmentosa	rs767882032, rs786204428, rs121908142, rs111033267, rs374963432, rs373208120, rs121908140, rs1576623563, rs374390376, rs746523071, rs376155416, rs201205811, rs1085307049, rs1231668679	N/A
Usher Syndrome	usher syndrome type 3, usher syndrome, Usher syndrome type 3A	rs1553776112, rs121908142, rs374963432, rs1553776052, rs933370216, rs1553776135, rs111033267, rs1576651623, rs373208120, rs201625237, rs121908140, rs1553772595, rs746523071, rs1576631624, rs1553776132 View all (11 more)	N/A

Show/Hide Unknown Diseases (1)

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.
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Albinism	Associate	39596324
Ciliopathies	Associate	39596324
Cone Rod Dystrophies	Associate	35481838
Deafness	Associate	39304915
Gyrate Atrophy	Associate	39596324
Hearing Loss Sensorineural	Associate	39304915
Oculocutaneous albinism type 2	Associate	10745043
Retinal Dystrophies	Associate	31968401, 39304915, 39596324
Retinitis Pigmentosa	Associate	26338283, 29545425, 31960602, 31968401
RHYNS syndrome	Associate	39596563
Usher syndrome type 1B	Associate	22681893
Usher Syndromes	Associate	19753315, 20717163, 22681893, 22964989, 23304067, 25404053, 25804404, 26338283, 28469144, 35481838, 39304915, 39337481, 9719374

CLRN1 (clarin 1)