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	7401
Gene name	Clarin 1
Gene symbol	CLRN1
Synonyms (NCBI Gene)	RP61USH3USH3A
Chromosome	3
Chromosome location	3q25.1
Summary	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

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

323

Show/Hide Causal Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
CLRN1-related disorder	Likely pathogenic; Pathogenic	rs746523071, rs111033267	RCV003398866 RCV003407275
Hearing impairment	Likely pathogenic; Pathogenic	rs121908140, rs1553776135	RCV001375084 RCV001375069
Neuronal ceroid lipofuscinosis	Pathogenic; Likely pathogenic	rs2107927719, rs2472761635, rs2472830838, rs1715594024	RCV005635607 RCV005636943 RCV005632688 RCV005633877
Rare genetic deafness	Pathogenic; Likely pathogenic	rs786204428, rs111033267, rs111033434, rs397517932, rs374963432	RCV000844691 RCV000844690 RCV000041430 RCV000844625 RCV000844624
Retinal dystrophy	Pathogenic; Likely pathogenic	rs762606406, rs746523071, rs786204428, rs878853379, rs2472830632, rs374390376, rs1235835151, rs1715594024, rs746128095	RCV004815586 RCV001073703 RCV001073424 RCV000225684 RCV003890841 RCV001073290 RCV001075319 RCV001073292 RCV003887969
Retinitis pigmentosa	Pathogenic; Likely pathogenic	rs762606406, rs121908140, rs111033267, rs1576623563	RCV002506728 RCV002496258 RCV000505037 RCV000787816
Retinitis pigmentosa 61	Pathogenic; Likely pathogenic	rs762606406, rs752910161, rs1380661508, rs745585873, rs1329440649, rs746523071, rs786204428, rs1463067573, rs121908140, rs1085307049, rs121908142, rs111033267, rs2107927719, rs2472831349, rs2472831271 View all (21 more)	RCV002506728 RCV003469761 RCV003470922 RCV003471164 RCV005032114 RCV002466459 RCV003468834 RCV003466001 RCV002496258 RCV004566682 RCV003466813 RCV003466814 RCV004571222 RCV003465824 RCV005034454 RCV003468480 RCV003468481 RCV003468482 RCV003468483 RCV003468484 RCV003468485 RCV003468486 RCV003468487 RCV003468488 RCV003468489 RCV003468490 RCV004574122 RCV004575667 RCV004575669 RCV003470355 RCV000023538 RCV003465476 RCV005031479 RCV005031480 RCV003466890 RCV003467324 RCV003467372 RCV003467418 RCV004570414 RCV005038009
Usher syndrome	Pathogenic; Likely pathogenic	rs762606406, rs1380661508, rs2107927808, rs746523071, rs397517932, rs374963432, rs746128095, rs1715589813	RCV004770188 RCV001806792 RCV005238105 RCV002281991 RCV002273943 RCV001582535 RCV004690033 RCV002274178
Usher syndrome type 3	Likely pathogenic; Pathogenic	rs746523071, rs786204428, rs121908140, rs121908141, rs1085307049, rs121908142, rs111033267, rs1553776036, rs201205811, rs376155416, rs397517932, rs374963432, rs1559982739, rs933370216, rs1576651623 View all (3 more)	RCV000169229 RCV000169027 RCV000004642 RCV000004643 RCV000004644 RCV000004646 RCV000004647 RCV000004648 RCV005616648 RCV000667382 RCV000041435 RCV000041436 RCV000782282 RCV000791320 RCV000987346 RCV001002692 RCV001002950 RCV001002951 RCV001199960
Usher syndrome type 3A	Pathogenic; Likely pathogenic	rs762606406, rs2107927490, rs1380661508, rs1329440649, rs746523071, rs786204428, rs121908140, rs111033267, rs373208120, rs1057516687, rs1057517224, rs376155416, rs1553776061, rs1553776112, rs1553776052 View all (9 more)	RCV002506728 RCV001823290 RCV005038333 RCV005032114 RCV001273481 RCV005003514 RCV002496258 RCV001376502 RCV005034454 RCV001273480 RCV005430310 RCV005430336 RCV005034244 RCV005430706 RCV005430810 RCV005430754 RCV005430692 RCV005430755 RCV005430586 RCV005031479 RCV005031480 RCV002243688 RCV005036155 RCV005038009 RCV001280869

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Melnick-Fraser syndrome	Uncertain significance	rs776997657	RCV001375119
Optic atrophy	Uncertain significance	rs567709615	RCV004816365
Retinitis Pigmentosa, Dominant	Conflicting classifications of pathogenicity; Uncertain significance; Benign	rs34027634, rs550716419	RCV000321689 RCV000288081 RCV000376478 RCV000316048 RCV000346639 RCV000367469
Retinitis pigmentosa-deafness syndrome	Conflicting classifications of pathogenicity; Uncertain significance; Benign	rs34027634, rs550716419	RCV000285424 RCV000352316 RCV000291402 RCV000379991 RCV000394325 RCV000389960

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)