Gene Gene information from NCBI Gene database.
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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
58
miRTarBase ID miRNA Experiments Reference
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
606397 12605 ENSG00000163646
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
18
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
CLRN1-related disorder Likely pathogenic; Pathogenic rs746523071, rs111033267 RCV003398866
RCV003407275
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hearing impairment Likely pathogenic; Pathogenic rs121908140, rs1553776135 RCV001375084
RCV001375069
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neuronal ceroid lipofuscinosis Pathogenic; Likely pathogenic rs2107927719, rs2472761635, rs2472830838, rs1715594024 RCV005635607
RCV005636943
RCV005632688
RCV005633877
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rare genetic deafness Pathogenic; Likely pathogenic rs786204428, rs111033267, rs111033434, rs397517932, rs374963432 RCV000844691
RCV000844690
RCV000041430
RCV000844625
RCV000844624
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
BRANCHIO-OTO-RENAL SYNDROME Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Melnick-Fraser syndrome Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Optic atrophy Uncertain significance ClinVar
Disgenet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
RETINITIS PIGMENTOSA 1 CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Albinism Albinism Pubtator 39596324 Associate
★☆☆☆☆
Found in Text Mining only
Alopecia Alopecia BEFREE 22787034, 26180195
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Astigmatism Astigmatism HPO_DG
★☆☆☆☆
Found in Text Mining only
Cataract Cataract BEFREE 22938382
★☆☆☆☆
Found in Text Mining only
Cataract Cataract HPO_DG
★☆☆☆☆
Found in Text Mining only
Ciliopathies Ciliopathy Pubtator 39596324 Associate
★☆☆☆☆
Found in Text Mining only
Ciliopathies Ciliopathies GENOMICS_ENGLAND_DG
★☆☆☆☆
Found in Text Mining only
Conductive hearing loss Hearing Loss HPO_DG
★☆☆☆☆
Found in Text Mining only
Congenital cataract Congenital Cataract BEFREE 20236115
★☆☆☆☆
Found in Text Mining only