USH1C (USH1 protein network component harmonin)

Gene

• Entrez ID: 10083
• Gene name: USH1 protein network component harmonin
• Gene symbol: USH1C
• Synonyms (NCBI Gene): AIE-75, DFNB18, DFNB18A, NY-CO-37, NY-CO-38, PDZ-45, PDZ-73, PDZ-73/NY-CO-38, PDZ73, PDZD7C, ush1cpst
• Chromosome: 11
• Chromosome location: 11p15.1
• Summary: 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

SNPs

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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 605242
• HGNC: 12597
• e!Ensembl: 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

Associated diseases

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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Autosomal recessive nonsyndromic hearing loss 18A	Pathogenic; Likely pathogenic	rs1290295453, rs1246699436, rs1278026061, rs756032457, rs397515359, rs1403777293, rs2133927984, rs766327614, rs2133917820, rs1364331716, rs1850950786, rs1283092935, rs1381315419, rs2497242255, rs1480243085, rs151045328, rs121908370, rs2497155607, rs1850985627, rs746871920, rs1565047971, rs2497241574, rs748171099, rs2496984080, rs1427085382, rs1850715505, rs769420899, rs138138689, rs377145777, rs1064797153, rs1355262412, rs397514500, rs762551629, rs1366154374, rs1465352266, rs778110397, rs745622612, rs1187887456, rs1298596518, rs1223763703, rs758555088, rs147956944, rs1482487617, rs1554965967, rs1554954574, rs1207247951, rs1554960388, rs1554960390, rs771279169, rs1554961152, rs1317951509, rs1554953745, rs1554953746, rs921755529, rs1554954681, rs1358056232, rs1389725640, rs765346539, rs775496999, rs1554961872, rs1287021691, rs1591961566, rs1565017125, rs1591999307, rs1850678559, rs1850741468, rs371257969	RCV003469561 RCV003462942 RCV003463038 RCV003469737 RCV003469667 RCV003462976 RCV001809331 RCV003471069 RCV003471063 RCV002272821 RCV004571170 RCV003465989 RCV005042936 RCV003464581 RCV005041990 RCV000984011 RCV000763237 RCV000983994 RCV003464633 RCV003328142 RCV003464770 RCV003464775 RCV003464776 RCV003464778 RCV003466497 RCV004573812 RCV004573813 RCV004573814 RCV003328125 RCV000409966 RCV000672216 RCV000673343 RCV000662094 RCV000984229 RCV000670352 RCV000673327 RCV000666443 RCV000669692 RCV000669103 RCV000669773 RCV000672382 RCV000670894 RCV000666800 RCV000666962 RCV000671298 RCV000669702 RCV000668048 RCV000670807 RCV000671259 RCV000669236 RCV000669286 RCV000674242 RCV000666602 RCV000669659 RCV000672856 RCV000674078 RCV000668530 RCV000669682 RCV000669950 RCV000674234 RCV000672492 RCV000668959 RCV000669966 RCV000671948 RCV000770885 RCV000770884 RCV003461077 RCV005047192 RCV005047290 RCV003462789	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hearing impairment	Likely pathogenic; Pathogenic	rs1850678559	RCV001375345	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hearing loss, autosomal recessive	Pathogenic	rs397515359, rs377145777	RCV001291493 RCV001291494	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rare genetic deafness	Pathogenic	rs397515359, rs151045328	RCV000824775 RCV000824776	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic; Likely pathogenic	rs1480243085, rs397515359, rs1850697098, rs1850741468	RCV004814836 RCV001073457 RCV001073238 RCV001073795	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa	Pathogenic	rs397515359, rs1207247951	RCV000787893 RCV001003245	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
USH1C-related disorder	Pathogenic; Likely pathogenic	rs397515359, rs151045328, rs762551629, rs758555088, rs138138689	RCV004755713 RCV004755714 RCV004755980 RCV003403559 RCV004756004	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher syndrome	Pathogenic; Likely pathogenic	rs397515359, rs151045328, rs2497240788, rs2497163167, rs1355262412, rs1482487617	RCV000505081 RCV000504855 RCV003389519 RCV003389533 RCV000504842 RCV004768539	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher syndrome type 1	Likely pathogenic; Pathogenic	rs766327614, rs1480243085, rs397515359, rs55983148, rs151045328, rs121908370, rs397514500, rs138138689, rs1317951509	RCV005397160 RCV001003246 RCV000213574 RCV000218261 RCV000220605 RCV000763238 RCV000662095 RCV002499156 RCV001004554	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher syndrome type 1C	Likely pathogenic; Pathogenic	rs761465345, rs2133927984, rs766327614, rs2133917820, rs1364331716, rs2497241282, rs2496999266, rs2496983878, rs2497155760, rs2497156421, rs2497003503, rs2497223524, rs2497155958, rs2497155740, rs2497241170, rs2496983474, rs2497187064, rs2497223701, rs1850950786, rs1381315419, rs1480243085, rs397515359, rs55983148, rs151045328, rs1403777293, rs121908370, rs876657624, rs748171099, rs2496984080, rs2497241374, rs2497073190, rs754257195, rs1427085382, rs138138689, rs377145777, rs1064797153, rs1355262412, rs397514500, rs778110397, rs762551629, rs1366154374, rs1465352266, rs745622612, rs1187887456, rs1298596518, rs1223763703, rs758555088, rs147956944, rs1482487617, rs1554965967, rs1554954574, rs1207247951, rs1554960388, rs1554960390, rs771279169, rs1554961152, rs1283092935, rs1317951509, rs1554953745, rs1554953746, rs921755529, rs1554954681, rs1358056232, rs1389725640, rs765346539, rs775496999, rs1554961872, rs1287021691, rs1850678559, rs1850741468	RCV001808890 RCV005868374 RCV005397160 RCV005042526 RCV005050552 RCV002306741 RCV002306754 RCV002306812 RCV002309554 RCV002309557 RCV002309758 RCV002309998 RCV002309090 RCV002307166 RCV002307324 RCV002310143 RCV002310509 RCV002310518 RCV002308391 RCV002466904 RCV005042936 RCV000005447 RCV000005448 RCV000005449 RCV000005450 RCV000005451 RCV000005453 RCV000240666 RCV005608975 RCV005047618 RCV005609067 RCV004576168 RCV004576169 RCV005040699 RCV000411458 RCV000412375 RCV000672216 RCV000673343 RCV000032622 RCV000032623 RCV000984228 RCV000670352 RCV000673327 RCV000666443 RCV000669692 RCV000669103 RCV000669773 RCV000672382 RCV000670894 RCV000666800 RCV000666962 RCV000671298 RCV000669702 RCV000668048 RCV000670807 RCV000671259 RCV000669236 RCV000669286 RCV000674242 RCV000666602 RCV000669659 RCV000672856 RCV000674078 RCV000668530 RCV000669682 RCV000669950 RCV000674234 RCV000672492 RCV000668959 RCV000669966 RCV000671948 RCV005047192 RCV005047290 RCV005633969	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher syndrome type 2	Likely pathogenic; Pathogenic	rs1064797153, rs1850678559, rs1850961650	RCV001199564 RCV001199565 RCV001199563	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTOSOMAL RECESSIVE ISOLATED SENSORINEURAL DEAFNESS TYPE DFNB	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	-	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL RECESSIVE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL RECESSIVE 18	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL RECESSIVE 18A	—	CTD, HPO CTD, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Meniere disease	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Optic atrophy	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis pigmentosa-deafness syndrome	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENSORINEURAL HEARING LOSS OF BILATERAL EARS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE 1B	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE 1C	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE I	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE IC	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma of large intestine	Colorectal Cancer	BEFREE	15219944		★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autosomal recessive non-syndromic sensorineural deafness type DFNB	Non-Syndromic Sensorineural Deafness	Orphanet			★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	29215599	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Clumsiness - motor delay	Motor delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	10209257, 10500064		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	37535601	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Hyperinsulinism	Congenital hyperinsulinism	Pubtator	23150283	Associate	★☆☆☆☆ Found in Text Mining only
Congenital sensorineural hearing loss	Congenital Sensorineural Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Deafness	Deafness	Pubtator	17407589, 23251578, 28653419, 28660889, 29434063, 33095980, 33724713	Associate	★☆☆☆☆ Found in Text Mining only
Deafness, Autosomal Recessive 18	Deafness	CLINVAR_DG	10973248, 11139240, 12107438, 12136232, 12630964, 15578223, 17407589, 20671281, 21203349, 21487335, 22135276, 23251578, 24416283, 24498627, 25356976, 25468891, 25525159, 25560255, 27460420, 27957503, 28041643		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Deafness, Autosomal Recessive 18	Deafness	GENOMICS_ENGLAND_DG	9760205		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Deafness, Autosomal Recessive 18	Deafness	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Depressive disorder	Mental Depression	HPO_DG			★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hallucinations	Hallucinations	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	23122587, 23150283, 23251578, 32991204, 33095980, 33231815, 34194829	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	20146813, 23251578	Associate	★☆☆☆☆ Found in Text Mining only
Hemianopsia	Hemianopsia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hereditary retinal dystrophy	Hereditary Retinal Dystrophy	CLINGEN_DG	10973247, 10973248, 11239869, 21203349		★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	29215599	Associate	★☆☆☆☆ Found in Text Mining only
Insulin-dependent diabetes mellitus secretory diarrhea syndrome	Insulin-Dependent Diabetes Mellitus Secretory Diarrhea Syndrome	BEFREE	21741320		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Intestinal Diseases	BEFREE	21741320		★☆☆☆☆ Found in Text Mining only
Kidney Neoplasms	Kidney neoplasm	Pubtator	29215599	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of kidney	Kidney Cancer	BEFREE	10209257		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	10209257, 10500064		★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Nonsyndromic Deafness	BEFREE	10973247, 12107438, 13680526, 16301217		★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Nonsyndromic Deafness	CLINGEN_DG	10973247, 12107438, 12136232, 14519688, 19324851		★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Renal carcinoma	Renal Carcinoma	BEFREE	10209257		★☆☆☆☆ Found in Text Mining only
Retinal Degeneration	Retinal degeneration	Pubtator	17407589	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	BEFREE	15645695		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	21487335		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	23150283, 23251578, 32795431	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	CLINVAR_DG	30718709		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	10571079, 23251578		★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Subcortical cerebral atrophy	Subcortical cerebral atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Usher Syndrome	Usher Syndrome	CLINVAR_DG	10973248		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher Syndrome	Usher Syndrome	LHGDN	12107438		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher Syndrome	Usher Syndrome	BEFREE	12702164, 19028668, 20142502, 20440071, 21203349, 23380860, 24725409, 29142287, 9445488		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher syndrome type 1	Usher Syndrome	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher syndrome type 1B	Usher syndrome	Pubtator	16679490, 17407589, 21203349, 22219650	Associate	★☆☆☆☆ Found in Text Mining only
Usher syndrome type 1C	Usher syndrome	Pubtator	9445488	Associate	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Usher syndrome, type 1A	Usher Syndrome	BEFREE	12588794, 12630964, 12702164, 15645695, 20052763, 28653419		★☆☆☆☆ Found in Text Mining only
Usher syndrome, type 1A	Usher Syndrome	GENOMICS_ENGLAND_DG	21203349		★☆☆☆☆ Found in Text Mining only
Usher syndrome, type 1B	Usher Syndrome	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher syndrome, type 1C	Usher Syndrome	BEFREE	10973247, 10973248, 28633508, 29037661		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher syndrome, type 1C	Usher Syndrome	CTD_human_DG	12136232		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndrome, Type I	Usher Syndrome	BEFREE	10973247, 12588794, 12630964, 12702164, 15590703, 20052763, 20142502, 21203349, 22219650, 23045546, 28653419, 8825055		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndrome, Type I	Usher Syndrome	CLINVAR_DG	10973247, 10973248, 11139240, 11810303, 12107438, 12630964, 12702164, 15578223, 21569298		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndrome, Type I	Usher Syndrome	CLINGEN_DG	10973247, 10973248, 11239869, 21203349		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE I, FRENCH VARIETY, FORMERLY	Usher Syndrome	CLINGEN_DG	10973247, 10973248, 11239869, 21203349		★☆☆☆☆ Found in Text Mining only
USHER SYNDROME, TYPE IA, FORMERLY	Usher Syndrome	CLINGEN_DG	10973247, 10973248, 11239869, 21203349		★☆☆☆☆ Found in Text Mining only
USHER SYNDROME, TYPE IB (disorder)	Usher Syndrome	CLINGEN_DG	10973247, 10973248, 11239869, 21203349		★☆☆☆☆ Found in Text Mining only
USHER SYNDROME, TYPE IC	Usher Syndrome	CLINVAR_DG	11139240, 12107438, 17407589, 21203349, 21487335, 22135276, 23251578, 24416283, 24498627, 25356976, 25468891, 25525159, 27440999, 27460420, 27957503, 28041643		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE IC	Usher Syndrome	BEFREE	11239869, 11810303, 12107438, 12136232, 28165476, 29037661, 29985171, 9238080		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE IC	Usher Syndrome	GENOMICS_ENGLAND_DG	9760205		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndromes	Usher syndrome	Pubtator	22135276, 23251578, 25404053, 27440999, 28653419, 35997788, 36011334, 8825055	Associate	★☆☆☆☆ Found in Text Mining only
Usher Syndromes	Usher syndrome	Pubtator	8128966	Stimulate	★☆☆☆☆ Found in Text Mining only
Vestibular Diseases	Vestibular disease	Pubtator	23251578	Associate	★☆☆☆☆ Found in Text Mining only