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.	10083
Gene name Gene Name - the full gene name approved by the HGNC.	USH1 protein network component harmonin
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	USH1C
Synonyms (NCBI Gene) Gene synonyms aliases	AIE-75, DFNB18, DFNB18A, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, PDZD7C, ush1cpst
Chromosome Chromosome number	11
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	11p15.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a scaffold protein that functions in the assembly of Usher protein complexes. The protein contains PDZ domains, a coiled-coil region with a bipartite nuclear localization signal and a PEST degradation sequence. Defects in this gene are t

Show/Hide all(66)

SNP ID	Visualize variation	Clinical significance	Consequence
rs41282932	G>A,C,T	Likely-benign, uncertain-significance, pathogenic	Coding sequence variant, intron variant, missense variant, genic downstream transcript variant
rs55983148	CCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTC>-,CCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCA	Benign, conflicting-interpretations-of-pathogenicity	Intron variant
rs121908370	G>A,C	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant
rs138138689	C>A,G,T	Pathogenic	Splice donor variant
rs140869579	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs143160805	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, genic downstream transcript variant, intron variant, missense variant
rs144761543	G>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs146333270	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, genic downstream transcript variant, intron variant, missense variant
rs146451547	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance, pathogenic	Genic downstream transcript variant, coding sequence variant, intron variant, stop gained, 3 prime UTR variant
rs147956944	T>G	Likely-pathogenic	Splice acceptor variant
rs148477093	G>A,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, genic downstream transcript variant, synonymous variant, coding sequence variant, non coding transcript variant
rs149510892	G>A,C	Benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, intron variant, missense variant, coding sequence variant
rs150567427	C>T	Uncertain-significance, pathogenic, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, splice acceptor variant, intron variant, 3 prime UTR variant
rs150593932	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs151045328	C>T	Likely-pathogenic, pathogenic	Non coding transcript variant, synonymous variant, coding sequence variant
rs151251262	G>A,C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, genic downstream transcript variant, synonymous variant, coding sequence variant
rs199739341	G>A,C	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs202095395	C>T	Benign-likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant
rs369021714	A>G	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, 3 prime UTR variant, coding sequence variant, synonymous variant, intron variant
rs377145777	G>A	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs397514500	C>A,G,T	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs397515359	->G	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs397517880	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, non coding transcript variant
rs758555088	->T	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, frameshift variant, non coding transcript variant
rs762551629	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant, stop gained, non coding transcript variant
rs767767573	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant, stop gained, coding sequence variant, genic downstream transcript variant
rs771279169	C>T	Likely-pathogenic	Splice acceptor variant
rs775496999	C>A,T	Likely-pathogenic	Splice donor variant
rs776511246	C>T	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs777591673	T>C	Uncertain-significance, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs778110397	C>A,G,T	Pathogenic, likely-pathogenic	Genic downstream transcript variant, splice acceptor variant
rs876657624	G>A,C,T	Likely-benign, pathogenic	Synonymous variant, stop gained, missense variant, non coding transcript variant, coding sequence variant
rs921755529	T>C	Likely-pathogenic	Genic downstream transcript variant, splice acceptor variant
rs1060499916	C>G,T	Pathogenic, uncertain-significance	Non coding transcript variant, genic downstream transcript variant, splice donor variant
rs1064797153	CTGCGGCT>-	Likely-pathogenic	Non coding transcript variant, intron variant, coding sequence variant, frameshift variant
rs1187887456	C>A	Likely-pathogenic	Splice acceptor variant
rs1207247951	C>-	Pathogenic	Coding sequence variant, intron variant, frameshift variant, non coding transcript variant
rs1223763703	G>T	Likely-pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1244378437	C>A,T	Pathogenic	Stop gained, coding sequence variant, intron variant, missense variant, non coding transcript variant
rs1283092935	C>G,T	Likely-pathogenic	Splice donor variant
rs1287021691	C>T	Likely-pathogenic	Splice donor variant
rs1298596518	A>C	Likely-pathogenic	Splice donor variant
rs1317951509	C>T	Likely-pathogenic, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs1355262412	CCTCCAATCCCACCTCA>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, intron variant, splice donor variant
rs1358056232	T>C	Likely-pathogenic	Splice acceptor variant, genic downstream transcript variant
rs1403777293	C>A,T	Pathogenic	Splice donor variant
rs1465352266	T>C,G	Likely-pathogenic	Splice acceptor variant, genic downstream transcript variant
rs1480243085	T>-	Pathogenic	Splice acceptor variant
rs1482487617	C>T	Likely-pathogenic	Splice donor variant
rs1554953350	C>A	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs1554953745	A>C,G	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs1554953746	C>A	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs1554954574	C>T	Likely-pathogenic	Splice acceptor variant, genic downstream transcript variant
rs1554954681	A>G	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs1554954858	A>G	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs1554957167	->G	Uncertain-significance, pathogenic	Coding sequence variant, frameshift variant, intron variant, genic downstream transcript variant
rs1554960388	->T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554960390	G>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1554961152	C>T	Likely-pathogenic	Splice donor variant
rs1554961872	C>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, splice donor variant
rs1554965967	T>C	Likely-pathogenic	Missense variant, initiator codon variant, non coding transcript variant
rs1565017125	C>A	Pathogenic	Splice acceptor variant, genic downstream transcript variant
rs1565058763	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1591961566	CA>-	Likely-pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs1591999307	C>T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs1592002789	C>G	Pathogenic	Intron variant

Show/Hide all(39)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016712	hsa-miR-335-5p	Microarray	18185580
MIRT1477175	hsa-miR-1825	CLIP-seq
MIRT1477176	hsa-miR-185	CLIP-seq
MIRT1477177	hsa-miR-199a-5p	CLIP-seq
MIRT1477178	hsa-miR-199b-5p	CLIP-seq
MIRT1477179	hsa-miR-3188	CLIP-seq
MIRT1477180	hsa-miR-3925-3p	CLIP-seq
MIRT1477181	hsa-miR-4306	CLIP-seq
MIRT1477182	hsa-miR-4454	CLIP-seq
MIRT1477183	hsa-miR-4534	CLIP-seq
MIRT1477184	hsa-miR-4644	CLIP-seq
MIRT1477185	hsa-miR-508-5p	CLIP-seq
MIRT1477186	hsa-miR-599	CLIP-seq
MIRT2462989	hsa-miR-142-3p	CLIP-seq
MIRT2462990	hsa-miR-3183	CLIP-seq
MIRT2462991	hsa-miR-3922-5p	CLIP-seq
MIRT2462992	hsa-miR-3929	CLIP-seq
MIRT2462993	hsa-miR-4419b	CLIP-seq
MIRT2462994	hsa-miR-4478	CLIP-seq
MIRT2462995	hsa-miR-4723-3p	CLIP-seq
MIRT2462996	hsa-miR-4757-5p	CLIP-seq
MIRT2462997	hsa-miR-513c	CLIP-seq
MIRT2462998	hsa-miR-514b-5p	CLIP-seq
MIRT2462999	hsa-miR-644	CLIP-seq
MIRT2463000	hsa-miR-648	CLIP-seq
MIRT2463001	hsa-miR-663b	CLIP-seq
MIRT2462989	hsa-miR-142-3p	CLIP-seq
MIRT2462990	hsa-miR-3183	CLIP-seq
MIRT2462991	hsa-miR-3922-5p	CLIP-seq
MIRT2462992	hsa-miR-3929	CLIP-seq
MIRT2462993	hsa-miR-4419b	CLIP-seq
MIRT2462994	hsa-miR-4478	CLIP-seq
MIRT2462995	hsa-miR-4723-3p	CLIP-seq
MIRT2462996	hsa-miR-4757-5p	CLIP-seq
MIRT2462997	hsa-miR-513c	CLIP-seq
MIRT2462998	hsa-miR-514b-5p	CLIP-seq
MIRT2462999	hsa-miR-644	CLIP-seq
MIRT2463000	hsa-miR-648	CLIP-seq
MIRT2463001	hsa-miR-663b	CLIP-seq

Show/Hide all(53)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000086	Process	G2/M transition of mitotic cell cycle	IMP	15219944
GO:0001750	Component	Photoreceptor outer segment	IEA
GO:0001750	Component	Photoreceptor outer segment	ISS
GO:0001917	Component	Photoreceptor inner segment	IBA
GO:0001917	Component	Photoreceptor inner segment	IEA
GO:0001917	Component	Photoreceptor inner segment	ISS
GO:0002093	Process	Auditory receptor cell morphogenesis	IBA
GO:0002142	Component	Stereocilia ankle link complex	IBA
GO:0005515	Function	Protein binding	IPI	11311560, 16301216, 16464467, 20142502, 24725409, 25416956, 25502805, 26812018, 27173435, 28514442, 29997244, 31515488, 32296183, 32814053, 33961781
GO:0005737	Component	Cytoplasm	IDA	10209257
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	ISS
GO:0005902	Component	Microvillus	IDA	24725409, 32209652
GO:0005902	Component	Microvillus	IEA
GO:0005903	Component	Brush border	IDA	21330445, 24725409
GO:0005903	Component	Brush border	IEA
GO:0005929	Component	Cilium	IBA
GO:0007605	Process	Sensory perception of sound	IBA
GO:0007605	Process	Sensory perception of sound	IEA
GO:0007605	Process	Sensory perception of sound	IMP	11398101
GO:0030046	Process	Parallel actin filament bundle assembly	ISS
GO:0030154	Process	Cell differentiation	IEA
GO:0030507	Function	Spectrin binding	IDA	23704327
GO:0032420	Component	Stereocilium	IEA
GO:0032420	Component	Stereocilium	ISS
GO:0032420	Component	Stereocilium	TAS	16464467
GO:0032426	Component	Stereocilium tip	IBA
GO:0032532	Process	Regulation of microvillus length	ISS
GO:0042472	Process	Inner ear morphogenesis	ISS
GO:0042491	Process	Inner ear auditory receptor cell differentiation	ISS
GO:0042995	Component	Cell projection	IEA
GO:0045177	Component	Apical part of cell	IDA	10209257
GO:0045202	Component	Synapse	ISS
GO:0045494	Process	Photoreceptor cell maintenance	IMP	11398101
GO:0046549	Process	Retinal cone cell development	IBA
GO:0050885	Process	Neuromuscular process controlling balance	IEA
GO:0050953	Process	Sensory perception of light stimulus	IMP	11398101
GO:0050957	Process	Equilibrioception	IMP	10973247
GO:0051017	Process	Actin filament bundle assembly	ISS
GO:0060122	Process	Inner ear receptor cell stereocilium organization	IBA
GO:0060122	Process	Inner ear receptor cell stereocilium organization	ISS
GO:0065003	Process	Protein-containing complex assembly	IDA	26812018
GO:1904106	Process	Protein localization to microvillus	IEA
GO:1904106	Process	Protein localization to microvillus	IMP	24725409, 26812018
GO:1904106	Process	Protein localization to microvillus	ISS
GO:1904970	Process	Brush border assembly	IDA	32209652
GO:1904970	Process	Brush border assembly	IEA
GO:1904970	Process	Brush border assembly	IMP	24725409
GO:1904970	Process	Brush border assembly	ISS

MIM	HGNC	e!Ensembl
605242	12597	ENSG00000006611

Protein

UniProt ID

Q9Y6N9

Protein name

Harmonin (Antigen NY-CO-38/NY-CO-37) (Autoimmune enteropathy-related antigen AIE-75) (Protein PDZ-73) (Renal carcinoma antigen NY-REN-3) (Usher syndrome type-1C protein)

Protein function

Anchoring/scaffolding protein that is a part of the functional network formed by USH1C, USH1G, CDH23 and MYO7A that mediates mechanotransduction in cochlear hair cells. Required for normal development and maintenance of cochlear hair cell bundle

PDB

1X5N , 2KBQ , 2KBR , 2KBS , 2LSR , 3K1R , 5F3X , 5MV8 , 5MV9 , 5XBF , 7X2E

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00595	PDZ	87 → 165	PDZ domain	Domain
PF00595	PDZ	211 → 290	PDZ domain	Domain
PF00595	PDZ	452 → 537	PDZ domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in small intestine, colon, kidney, eye and weakly in pancreas. Expressed also in vestibule of the inner ear. {ECO:0000269|PubMed:12588794}.

Sequence

MDRKVAREFRHKVDFLIENDAEKDYLYDVLRMYHQTMDVAVLVGDLKLVINEPSRLPLFD
AIRPLIPLKHQVEYDQLTPRRSRKLKEVRLDRLHPEGLGLSVRGGLEFGCGLFISHLIKG
GQADSVGLQVGDEIVRINGYSISSCTHEEVINLIRTKKTVSIKVRHIGLIPVKSSPDEPL
TWQYVDQFVSESGGVRGSLGSPGNRENKEKKVFISLVGSRGLGCSISSGPIQKPGIFISH
VKPGSLSAEVGLEIGDQIVEVNGVDFSNLDHKEAVNVLKSSRSLTISIVAAAGRELFMTD
RERLAEARQRELQRQELLMQKRLAMESNKILQEQQEMERQRRKEIAQKAAEENERYRKEM
EQIVEEEEKFKKQWEEDWGSKEQLLLPKTITAEVHPVPLRKPKYDQGVEPELEPADDLDG
GTEEQGEQDFRKYEEGFDPYSMFTPEQIMGKDVRLLRIKKEGSLDLALEGGVDSPIGKVV
VSAVYERGAAERHGGIVKGDEIMAINGKIVTDYTLAEAEAALQKAWNQGGDWIDLVVAVC
PPKEYDDELTFF

Sequence length

552

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
Deafness	Autosomal recessive nonsyndromic hearing loss 18A	rs775496999, rs1355262412, rs1591961566, rs121908370, rs1565017125, rs762551629, rs1207247951, rs1591999307, rs778110397, rs1554960388, rs1187887456, rs1554960390, rs138138689, rs1298596518, rs771279169 View all (10 more)	N/A
hearing impairment	Hearing impairment	rs1850678559	N/A
Hearing Loss	Hearing loss, autosomal recessive	rs397515359, rs377145777	N/A
retinal dystrophy	Retinal dystrophy	rs397515359, rs1480243085, rs1850697098, rs1850741468	N/A
Retinitis Pigmentosa	retinitis pigmentosa	rs1207247951, rs397515359	N/A
Usher Syndrome	Usher syndrome type 1C, usher syndrome type 2, usher syndrome type 1, usher syndrome	rs121908370, rs762551629, rs1207247951, rs778110397, rs876657624, rs1480243085, rs55983148, rs1850678559, rs138138689, rs151045328, rs1850961650, rs377145777, rs397515359, rs1317951509, rs147956944 View all (4 more)	N/A

Show/Hide Unknown Diseases (2)

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.
Meniere Disease	meniere disease	N/A	N/A	ClinVar
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (20)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Carcinoma Renal Cell	Associate	29215599
Colorectal Neoplasms	Associate	37535601
Congenital Hereditary and Neonatal Diseases and Abnormalities	Associate	28653419
Congenital Hyperinsulinism	Associate	23150283
Deafness	Associate	17407589, 23251578, 28653419, 28660889, 29434063, 33095980, 33724713
Hearing Loss	Associate	23122587, 23150283, 23251578, 32991204, 33095980, 33231815, 34194829
Hearing Loss Sensorineural	Associate	20146813, 23251578
Hypothyroidism Congenital Nongoitrous 1	Associate	23150283
Hypoxia	Associate	29215599
Immune Dysregulation Polyendocrinopathy Enteropathy X Linked Syndrome	Associate	24250806
Kidney Neoplasms	Associate	29215599
Nonsyndromic Deafness	Associate	13680526, 31858762
Retinal Degeneration	Associate	17407589
Retinitis Pigmentosa	Associate	23150283, 23251578, 32795431
Tooth Loss	Associate	28653419
Usher syndrome type 1B	Associate	16679490, 17407589, 21203349, 22219650
Usher syndrome type 1C	Associate	9445488
Usher Syndromes	Associate	22135276, 23251578, 25404053, 27440999, 28653419, 35997788, 36011334, 8825055
Usher Syndromes	Stimulate	8128966
Vestibular Diseases	Associate	23251578

USH1C (USH1 protein network component harmonin)