CLRN3

Summary

CLRN3 (clarin 3, HGNC:20795) is a protein-coding gene on chromosome 10q26.2, encoding Clarin-3 (Q8NCR9).

Predicted to be involved in sensory perception of sound. Located in extracellular exosome.

Source: NCBI Gene 119467 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 47 total — 1 pathogenic
• MANE Select transcript: NM_152311

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20795
Approved symbol	CLRN3
Name	clarin 3
Location	10q26.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC32871, USH3AL1
Ensembl gene	ENSG00000180745
Ensembl biotype	protein_coding
OMIM	620256
Entrez	119467

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000368671, ENST00000856088, ENST00000856089, ENST00000856090, ENST00000856091

RefSeq mRNA: 1 — MANE Select: NM_152311 NM_152311

CCDS: CCDS7656

Canonical transcript exons

ENST00000368671 — 3 exons

Exon	Start	End
ENSE00001279185	127883696	127883875
ENSE00001447723	127877841	127878420
ENSE00001447724	127892556	127892941

Expression profiles

Bgee: expression breadth ubiquitous, 103 present calls, max score 99.66.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3923 / max 132.1039, expressed in 48 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
111992	0.2187	39
111991	0.1021	24
111990	0.0716	21

Top tissues by expression

228 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	99.66	gold quality
jejunal mucosa	UBERON:0000399	98.92	gold quality
colonic mucosa	UBERON:0000317	98.59	gold quality
mucosa of sigmoid colon	UBERON:0004993	98.56	gold quality
mucosa of transverse colon	UBERON:0004991	97.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	97.25	gold quality
rectum	UBERON:0001052	96.64	gold quality
kidney epithelium	UBERON:0004819	94.85	silver quality
duodenum	UBERON:0002114	93.88	gold quality
pancreatic ductal cell	CL:0002079	92.32	gold quality
epithelial cell of pancreas	CL:0000083	91.35	silver quality
right lobe of liver	UBERON:0001114	90.10	gold quality
small intestine Peyer’s patch	UBERON:0003454	87.22	gold quality
liver	UBERON:0002107	86.73	gold quality
small intestine	UBERON:0002108	86.10	gold quality
gall bladder	UBERON:0002110	85.63	gold quality
transverse colon	UBERON:0001157	85.23	gold quality
adult mammalian kidney	UBERON:0000082	84.75	gold quality
jejunum	UBERON:0002115	79.76	gold quality
kidney	UBERON:0002113	79.46	gold quality
intestine	UBERON:0000160	77.52	gold quality
large intestine	UBERON:0000059	74.44	gold quality
vermiform appendix	UBERON:0001154	74.18	gold quality
colon	UBERON:0001155	73.36	gold quality
caecum	UBERON:0001153	72.79	gold quality
caput epididymis	UBERON:0004358	71.08	gold quality
cortex of kidney	UBERON:0001225	70.83	gold quality
islet of Langerhans	UBERON:0000006	68.46	gold quality
colonic epithelium	UBERON:0000397	68.02	gold quality
adult organism	UBERON:0007023	66.52	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting CLRN3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-4645-3P	99.76	69.33	993
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-6733-3P	99.54	67.80	1281
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-5100	99.11	67.52	1098
HSA-MIR-198	98.70	67.32	920
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-4433A-3P	97.75	62.82	1435
HSA-MIR-6793-3P	97.66	65.78	1084
HSA-MIR-510-5P	97.66	65.82	916
HSA-MIR-574-3P	92.35	64.27	41

Literature-anchored findings (GeneRIF, showing 1)

• The SNP rs6482992 in the CLRN3 gene had the smallest p value in analyses of the cognitive outcome. (PMID:22658654)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	clrn3	ENSDARG00000100465
mus_musculus	Clrn3	ENSMUSG00000050866
rattus_norvegicus	Clrn3	ENSRNOG00000028288
drosophila_melanogaster	CG1103	FBGN0037235
caenorhabditis_elegans		WBGENE00235279

Paralogs (2): CLRN1 (ENSG00000163646), CLRN2 (ENSG00000249581)

Protein

Protein identifiers

Clarin-3 — Q8NCR9 (reviewed: Q8NCR9)

Alternative names: Transmembrane protein 12, Usher syndrome type-3A-like protein 1

All UniProt accessions (1): Q8NCR9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the clarin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NCR9-1	1	yes
Q8NCR9-2	2

RefSeq proteins (1): NP_689524* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026748	Clarin	Family

Pfam: PF25807

UniProt features (10 total): transmembrane region 4, splice variant 2, sequence variant 2, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NCR9-F1	86.68	0.53

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 83

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GATA6_01, HNF4_DR1_Q3, HNF4_01, PPAR_DR1_Q2, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, AACTTT_UNKNOWN, GOBP_SENSORY_PERCEPTION, GATA1_02, VECCHI_GASTRIC_CANCER_EARLY_UP, VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN, GCNP_SHH_UP_LATE.V1_DN, CRX_DN.V1_DN, BARX1_TARGET_GENES, DLX2_TARGET_GENES

GO Biological Process (1): sensory perception of sound (GO:0007605)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): membrane (GO:0016020), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
sensory perception of mechanical stimulus	1
binding	1
cellular anatomical structure	1
extracellular vesicle	1

Protein interactions and networks

STRING

946 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLRN3	CACNG2	Q9Y698	717
CLRN3	TMIGD1	Q6UXZ0	623
CLRN3	ZNF614	Q8N883	537
CLRN3	CCNYL1	Q8N7R7	492
CLRN3	CBARP	Q8N350	491
CLRN3	UBOX5	O94941	481
CLRN3	SLC6A19	Q695T7	479
CLRN3	SLC5A1	P13866	476
CLRN3	MDP1	Q86V88	476
CLRN3	KCTD9	Q7L273	474
CLRN3	RNF24	Q9Y225	474
CLRN3	SLC10A2	Q12908	463
CLRN3	TUBG2	Q9NRH3	463
CLRN3	ZNF211	Q13398	461
CLRN3	FSIP2	Q5CZC0	456

IntAct

14 interactions, top by confidence:

A	B	Type	Score
CLRN3	NME2P1	psi-mi:“MI:0915”(physical association)	0.560
HTT	CLRN3	psi-mi:“MI:0915”(physical association)	0.560
CLRN3	HCCS	psi-mi:“MI:0915”(physical association)	0.400
ZDHHC17	CLRN3	psi-mi:“MI:0915”(physical association)	0.370
CLRN3	TXNDC9	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): CLRN3 (Two-hybrid), NME2P1 (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), TXNDC9 (Affinity Capture-MS), CCDC43 (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), HCCS (Affinity Capture-MS), GOLGA6A (Cross-Linking-MS (XL-MS)), PPAN (Cross-Linking-MS (XL-MS)), CLRN3 (Cross-Linking-MS (XL-MS)), CLRN3 (Cross-Linking-MS (XL-MS)), CLRN3 (Cross-Linking-MS (XL-MS)), CLRN3 (Cross-Linking-MS (XL-MS)), CLRN3 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A2R8RY99, A0PK11, A9UL59, B2RVW2, B4L184, B4LC58, B4N5D3, D3ZFW5, O95473, P23290, P35801, P35802, P35803, P36964, P36965, P51674, P56749, P58418, P79826, Q0IIL2, Q0P4G7, Q0VD07, Q11085, Q13491, Q2YDD6, Q53R12, Q5R603, Q5R9K1, Q5R9Q3, Q5R9R3, Q5T9L3, Q5ZLR1, Q6AYR5, Q6CRM6, Q6DID7, Q6P689, Q6UX40, Q754N9, Q7YWX7, Q812E9

Diamond homologs: Q6AYR5, Q8BHH8, Q8NCR9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

47 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	39
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1807724	GRCh37/hg19 10q26.2-26.3(chr10:128877896-131842835)x1	Pathogenic

SpliceAI

361 predictions. Top by Δscore:

Variant	Effect	Δscore
10:127878421:C:CC	acceptor_gain	0.9900
10:127891322:C:CT	acceptor_gain	0.9900
10:127892551:TTTA:T	donor_loss	0.9900
10:127892552:TTAC:T	donor_loss	0.9900
10:127892553:TACCT:T	donor_loss	0.9900
10:127892554:A:AT	donor_loss	0.9900
10:127878419:TG:T	acceptor_gain	0.9800
10:127883832:CGAA:C	acceptor_gain	0.9800
10:127892557:TGCAA:T	donor_gain	0.9800
10:127878416:GGATG:G	acceptor_gain	0.9400
10:127878417:GATG:G	acceptor_gain	0.9400
10:127878419:TGC:T	acceptor_loss	0.9400
10:127878421:CTGA:C	acceptor_loss	0.9400
10:127878422:T:G	acceptor_loss	0.9400
10:127892555:CCTG:C	donor_gain	0.9400
10:127878398:C:CT	acceptor_gain	0.9300
10:127878423:G:C	acceptor_loss	0.9300
10:127891325:A:C	acceptor_gain	0.9300
10:127878418:A:C	acceptor_gain	0.9200
10:127891323:A:C	acceptor_gain	0.9200
10:127883833:G:T	acceptor_gain	0.8900
10:127878418:ATG:A	acceptor_gain	0.8800
10:127883695:CCA:C	donor_gain	0.8800
10:127883692:TCAC:T	donor_gain	0.8700
10:127883693:CACC:C	donor_gain	0.8700
10:127883694:ACCA:A	donor_gain	0.8700
10:127883695:CCAC:C	donor_gain	0.8700
10:127892554:A:AC	donor_gain	0.8700
10:127892555:C:CC	donor_gain	0.8700
10:127878404:C:CT	acceptor_gain	0.8400

AlphaMissense

1478 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:127892746:G:C	S13R	0.984
10:127892746:G:T	S13R	0.984
10:127892748:T:G	S13R	0.984
10:127883784:G:C	S107R	0.980
10:127883784:G:T	S107R	0.980
10:127883786:T:G	S107R	0.980
10:127892688:A:G	W33R	0.979
10:127892688:A:T	W33R	0.979
10:127883760:G:C	S115R	0.975
10:127883760:G:T	S115R	0.975
10:127883762:T:G	S115R	0.975
10:127883711:A:G	W132R	0.974
10:127883711:A:T	W132R	0.974
10:127892734:G:C	S17R	0.973
10:127892734:G:T	S17R	0.973
10:127892736:T:G	S17R	0.973
10:127892677:A:C	S36R	0.972
10:127892677:A:T	S36R	0.972
10:127892679:T:G	S36R	0.972
10:127883805:A:C	S100R	0.970
10:127883805:A:T	S100R	0.970
10:127883807:T:G	S100R	0.970
10:127883763:G:C	N114K	0.968
10:127883763:G:T	N114K	0.968
10:127892755:G:C	F10L	0.965
10:127892755:G:T	F10L	0.965
10:127892757:A:G	F10L	0.965
10:127878287:G:C	F181L	0.963
10:127878287:G:T	F181L	0.963
10:127878289:A:G	F181L	0.963

dbSNP variants (sampled 300 via entrez): RS1000069840 (10:127886644 C>A,T), RS1000123173 (10:127886847 A>G), RS1000675344 (10:127892965 A>G), RS1000699834 (10:127882507 C>A,T), RS1000869913 (10:127883325 T>G), RS1001174127 (10:127893821 A>G,T), RS1001265676 (10:127894268 C>A), RS1001277045 (10:127894412 C>T), RS1001303860 (10:127883129 A>G), RS1001652632 (10:127879722 A>C), RS1001662477 (10:127879522 T>C), RS1001744837 (10:127887774 T>A), RS1001751396 (10:127888021 C>T), RS1001882982 (10:127879224 T>C), RS1002075431 (10:127889026 G>A)

Disease associations

OMIM: gene MIM:620256 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001546_3	Parkinson’s disease (motor and cognition)	4.000000e-06
GCST009391_3	Metabolite levels	9.000000e-06
GCST009391_467	Metabolite levels	7.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009777	citrulline measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	2
Aflatoxin B1	affects expression, decreases expression	2
methyleugenol	decreases expression	1
propionaldehyde	decreases expression	1
sodium arsenite	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
entinostat	decreases expression	1
belinostat	decreases expression	1
Rosiglitazone	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	decreases expression	1
Arsenic	affects methylation	1
Estradiol	decreases expression	1
Phenobarbital	affects expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Cyclosporine	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.