NPHP1 (nephrocystin 1)

Gene

• Entrez ID: 4867
• Gene name: Nephrocystin 1
• Gene symbol: NPHP1
• Synonyms (NCBI Gene): JBTS4, NPH1, SLSN1
• Chromosome: 2
• Chromosome location: 2q13
• Summary: This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs114250691	A>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs121907898	A>C,T	Pathogenic	Stop gained, coding sequence variant, missense variant
rs121907899	C>A,T	Pathogenic	Coding sequence variant, missense variant
rs140446520	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Coding sequence variant, intron variant, missense variant
rs140469160	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs141763330	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs144217506	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs144850331	C>G,T	Conflicting-interpretations-of-pathogenicity	3 prime UTR variant, synonymous variant, coding sequence variant, genic downstream transcript variant, downstream transcript variant
rs371112962	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, coding sequence variant
rs373915635	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs376974221	C>T	Pathogenic	Intron variant, splice donor variant
rs398123285	->G	Pathogenic	Coding sequence variant, frameshift variant
rs747861275	C>-	Pathogenic	Splice donor variant, genic downstream transcript variant
rs760619900	C>G	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, 3 prime UTR variant, downstream transcript variant, missense variant
rs763004817	T>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs765263671	G>A	Pathogenic	Coding sequence variant, stop gained
rs766524637	T>-,TT	Pathogenic	Frameshift variant, coding sequence variant
rs779032904	A>-	Conflicting-interpretations-of-pathogenicity	Intron variant, genic downstream transcript variant
rs1017750255	A>-	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs1233478832	C>A	Pathogenic	Splice donor variant, genic downstream transcript variant
rs1349732291	C>A	Pathogenic	Coding sequence variant, stop gained
rs1553484094	TC>-	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT670620	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT670619	hsa-miR-764	HITS-CLIP	23824327
MIRT670618	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT670617	hsa-miR-1224-3p	HITS-CLIP	23824327
MIRT670616	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT670615	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT670614	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT670613	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT670612	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT670611	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT670610	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT670608	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT679316	hsa-miR-3663-5p	HITS-CLIP	23824327
MIRT670607	hsa-miR-6790-3p	HITS-CLIP	23824327
MIRT670606	hsa-miR-6821-3p	HITS-CLIP	23824327
MIRT679315	hsa-miR-6131	HITS-CLIP	23824327
MIRT670604	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT670603	hsa-miR-640	HITS-CLIP	23824327
MIRT679314	hsa-miR-6843-3p	HITS-CLIP	23824327
MIRT679313	hsa-miR-6848-3p	HITS-CLIP	23824327
MIRT670620	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT670619	hsa-miR-764	HITS-CLIP	23824327
MIRT670618	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT670617	hsa-miR-1224-3p	HITS-CLIP	23824327
MIRT670616	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT670615	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT670614	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT670613	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT670612	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT670611	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT670610	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT670609	hsa-miR-150-5p	HITS-CLIP	23824327
MIRT670608	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT670607	hsa-miR-6790-3p	HITS-CLIP	23824327
MIRT670606	hsa-miR-6821-3p	HITS-CLIP	23824327
MIRT670605	hsa-miR-6778-3p	HITS-CLIP	23824327
MIRT670604	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT670603	hsa-miR-640	HITS-CLIP	23824327
MIRT670620	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT670619	hsa-miR-764	HITS-CLIP	23824327
MIRT670618	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT670617	hsa-miR-1224-3p	HITS-CLIP	23824327
MIRT670616	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT670615	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT670614	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT670613	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT670612	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT670611	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT670610	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT670608	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT679316	hsa-miR-3663-5p	HITS-CLIP	23824327
MIRT670607	hsa-miR-6790-3p	HITS-CLIP	23824327
MIRT670606	hsa-miR-6821-3p	HITS-CLIP	23824327
MIRT679315	hsa-miR-6131	HITS-CLIP	23824327
MIRT670604	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT670603	hsa-miR-640	HITS-CLIP	23824327
MIRT679314	hsa-miR-6843-3p	HITS-CLIP	23824327
MIRT679313	hsa-miR-6848-3p	HITS-CLIP	23824327
MIRT670620	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT670619	hsa-miR-764	HITS-CLIP	23824327
MIRT670618	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT670617	hsa-miR-1224-3p	HITS-CLIP	23824327
MIRT670616	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT670615	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT670614	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT670613	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT670612	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT670611	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT670610	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT670609	hsa-miR-150-5p	HITS-CLIP	23824327
MIRT670608	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT670607	hsa-miR-6790-3p	HITS-CLIP	23824327
MIRT670606	hsa-miR-6821-3p	HITS-CLIP	23824327
MIRT670605	hsa-miR-6778-3p	HITS-CLIP	23824327
MIRT670604	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT670603	hsa-miR-640	HITS-CLIP	23824327
MIRT1190697	hsa-miR-3137	CLIP-seq
MIRT1190698	hsa-miR-3686	CLIP-seq
MIRT1190699	hsa-miR-4307	CLIP-seq
MIRT1190700	hsa-miR-4446-5p	CLIP-seq
MIRT1190701	hsa-miR-4778-5p	CLIP-seq
MIRT2284161	hsa-miR-106a	CLIP-seq
MIRT2284162	hsa-miR-106b	CLIP-seq
MIRT2284163	hsa-miR-17	CLIP-seq
MIRT2284164	hsa-miR-20a	CLIP-seq
MIRT2284165	hsa-miR-20b	CLIP-seq
MIRT2284166	hsa-miR-3609	CLIP-seq
MIRT2284167	hsa-miR-382	CLIP-seq
MIRT2284168	hsa-miR-4645-3p	CLIP-seq
MIRT2284169	hsa-miR-4796-3p	CLIP-seq
MIRT2284170	hsa-miR-519d	CLIP-seq
MIRT2284171	hsa-miR-542-3p	CLIP-seq
MIRT2284172	hsa-miR-548ah	CLIP-seq
MIRT2284173	hsa-miR-93	CLIP-seq
MIRT2391695	hsa-miR-568	CLIP-seq
MIRT2391696	hsa-miR-944	CLIP-seq
MIRT1190697	hsa-miR-3137	CLIP-seq
MIRT1190698	hsa-miR-3686	CLIP-seq
MIRT1190699	hsa-miR-4307	CLIP-seq
MIRT1190700	hsa-miR-4446-5p	CLIP-seq
MIRT1190701	hsa-miR-4778-5p	CLIP-seq
MIRT1190697	hsa-miR-3137	CLIP-seq
MIRT1190698	hsa-miR-3686	CLIP-seq
MIRT1190699	hsa-miR-4307	CLIP-seq
MIRT1190700	hsa-miR-4446-5p	CLIP-seq
MIRT1190701	hsa-miR-4778-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005198	Function	Structural molecule activity	NAS	12006559
GO:0005515	Function	Protein binding	IPI	12244321, 12872122, 15661758, 16374509, 18633336, 20664800, 20856870, 21357692, 21565611, 21633164, 23532844, 25825872, 26638075, 27173435, 29959317, 33961781
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005911	Component	Cell-cell junction	IDA	21565611
GO:0005912	Component	Adherens junction	IEA
GO:0005923	Component	Bicellular tight junction	IEA
GO:0005929	Component	Cilium	IBA
GO:0005929	Component	Cilium	IEA
GO:0007165	Process	Signal transduction	NAS	12244321
GO:0007283	Process	Spermatogenesis	IEA
GO:0007632	Process	Visual behavior	NAS	12205563
GO:0016020	Component	Membrane	NAS	10665934
GO:0030030	Process	Cell projection organization	IEA
GO:0030030	Process	Cell projection organization	ISS
GO:0030036	Process	Actin cytoskeleton organization	NAS	12006559
GO:0030154	Process	Cell differentiation	IEA
GO:0031514	Component	Motile cilium	IDA	16885411
GO:0032391	Component	Photoreceptor connecting cilium	ISS
GO:0042995	Component	Cell projection	IEA
GO:0048515	Process	Spermatid differentiation	ISS
GO:0060041	Process	Retina development in camera-type eye	ISS
GO:0070161	Component	Anchoring junction	IEA
GO:0090251	Process	Protein localization involved in establishment of planar polarity	IBA
GO:0098609	Process	Cell-cell adhesion	NAS	12006559
GO:1903348	Process	Positive regulation of bicellular tight junction assembly	IMP	19755384

Other IDs

• MIM: 607100
• HGNC: 7905
• e!Ensembl: ENSG00000144061

Protein

• UniProt ID: O15259
• Protein name: Nephrocystin-1 (Juvenile nephronophthisis 1 protein)
• Protein function: Together with BCAR1 it may play a role in the control of epithelial cell polarity (By similarity). Involved in the organization of apical junctions in kidney cells together with NPHP4 and RPGRIP1L/NPHP8 (By similarity). Does not seem to be stric
• PDB: 1S1N, 6O1Q
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00018	SH3_1	158 → 204	SH3 domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Widespread expression, with highest levels in pituitary gland, spinal cord, thyroid gland, testis, skeletal muscle, lymph node and trachea. Weakly expressed in heart, kidney and pancreas. Expressed in nasal epithelial cells (at protein
• Sequence:

  MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENK
  NALQKLSKADESAPVANYNQRKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEE
  SESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAVGDFTAQQVGDLTFKKGEILL
  VIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV
  KQRTDPHWSAVQKAISEAGIFCLVNHVSFCYLIVLMRNRMETVEDTNGSETGFRAWNVQS
  RGRIFLVSKPVLQINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQL
  AFRDLMWDATEGTIRSRPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSN
  IHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFIRSNSASPDLGILFELGISYIRNST
  GERGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSVFYQI
  MTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQ
  STDLISHPMLATFPMLLEQPDVMDALRSSWAGKESTLKRSEKRDKEFLKSTFLLVYHDCV
  LPLLHSTRLPPFRWAEEETETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQT
  YDFLGEMRKNAV

• Sequence length: 732

Pathways

Reactome:

Anchoring of the basal body to the plasma membrane

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
Clear cell carcinoma of kidney	Pathogenic	rs121907899	RCV005887255	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital anomaly of kidney and urinary tract	Pathogenic	rs754137355	RCV001849622	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome and related disorders	Likely pathogenic; Pathogenic	rs752708835, rs564605452, rs376974221, rs1017750255	RCV002282819 RCV003155856 RCV003492029 RCV003155299	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome with renal defect	Pathogenic; Likely pathogenic	rs547352656, rs2104483923, rs376492641, rs1410236296, rs772720024, rs773781058, rs745806504, rs752708835, rs1233478832, rs121907899, rs367600757, rs1388373598, rs564605452, rs766524637, rs376974221, rs1193790186, rs1454994826, rs762322858, rs1327440899, rs1559043866, rs2467374890, rs369977541, rs1482624366, rs1679162266, rs2467132343, rs2467252177, rs2467252243, rs1482130141, rs2467259873, rs1435671751, rs2467251453, rs2467344481, rs2467332716, rs2467599617, rs1681356752, rs2467273765, rs2467238709, rs774810198, rs1210552017, rs2467599107, rs2467132150, rs2467251149, rs1336978749, rs2467354598, rs2467370218, rs2467370270, rs2467403268, rs2467251817, rs1683749371, rs2467272890, rs757139057, rs2467251559, rs765263671, rs1349732291, rs1017750255, rs1311042980, rs753517219, rs398123285	RCV001332330 RCV003469752 RCV003469780 RCV003469679 RCV004571682 RCV002492327 RCV002497908 RCV003471306 RCV003466796 RCV003466797 RCV003465966 RCV005021662 RCV003466028 RCV003463749 RCV002494861 RCV003471527 RCV003471528 RCV003471529 RCV003471530 RCV003471531 RCV003471532 RCV003471533 RCV003471534 RCV003463183 RCV003463184 RCV003471535 RCV003471536 RCV003471537 RCV003471538 RCV003471539 RCV003471540 RCV003471541 RCV003476576 RCV003463185 RCV003471542 RCV003471543 RCV003471544 RCV003463186 RCV003471545 RCV003463187 RCV003471546 RCV003471547 RCV003471548 RCV003471549 RCV003476577 RCV005014767 RCV005014801 RCV004574367 RCV004574368 RCV004574369 RCV004574370 RCV004574371 RCV002507229 RCV002493328 RCV003465664 RCV001260993 RCV002497439 RCV002505566 RCV004566944	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis	Pathogenic; Likely pathogenic	rs547352656, rs1683656584, rs2104483923, rs376492641, rs1410236296, rs772720024, rs773781058, rs1328879943, rs1680874514, rs2104480049, rs745806504, rs2104553788, rs1458494785, rs2104548314, rs752708835, rs1233478832, rs121907898, rs121907899, rs2467370400, rs367600757, rs1374365071, rs1388373598, rs370205671, rs2467370218, rs1486706164, rs2467403268, rs2467332466, rs2467621338, rs2467598236, rs2467259343, rs2467272833, rs2467395269, rs2467168254, rs766524637, rs376974221, rs1679162266, rs2467252243, rs1435671751, rs2467599617, rs1210552017, rs2467599107, rs2467251149, rs558873032, rs2467345309, rs772953015, rs2467118161, rs2467370270, rs2467405409, rs769143199, rs2467333810, rs2467231974, rs1559090282, rs2467333753, rs1682462329, rs759193940, rs2467119538, rs2467259533, rs1171179496, rs2467333098, rs1204764976, rs1683749371, rs747861275, rs765263671, rs1349732291, rs1017750255, rs1679148969, rs1311042980, rs1682584195, rs753517219, rs1679301117, rs764740388, rs398123285	RCV001382647 RCV001378712 RCV001389067 RCV001390765 RCV001382586 RCV001982565 RCV002011188 RCV002035279 RCV001964657 RCV001913291 RCV001970457 RCV001932927 RCV001960023 RCV001957637 RCV003586324 RCV001851623 RCV000234828 RCV000537800 RCV003068804 RCV003088842 RCV002612025 RCV002634387 RCV002576334 RCV002653965 RCV002801310 RCV002863746 RCV002852046 RCV002890327 RCV002908847 RCV002982965 RCV003007858 RCV003049397 RCV003032701 RCV000473574 RCV001859657 RCV005100196 RCV003748496 RCV003586426 RCV003586427 RCV003748497 RCV003748498 RCV003586518 RCV003586763 RCV003586822 RCV003587154 RCV003587549 RCV003587381 RCV003587796 RCV003587865 RCV003587935 RCV003749378 RCV003749459 RCV003749629 RCV003749552 RCV003749860 RCV003749948 RCV003750050 RCV003750195 RCV003747988 RCV003747948 RCV003749694 RCV005059555 RCV000550431 RCV000702943 RCV003748273 RCV001855653 RCV000791573 RCV001059300 RCV001059818 RCV001068170 RCV001039504 RCV001234710 RCV001239557 RCV001204206	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis 1	Pathogenic; Likely pathogenic	rs547352656, rs1410236296, rs773781058, rs745806504, rs1458494785, rs2104548702, rs2467403726, rs1233478832, rs121907898, rs121907899, rs367600757, rs1388373598, rs2467374878, rs766524637, rs376974221, rs1435671751, rs2467599617, rs2467405206, rs2467370270, rs2467403268, rs2467259314, rs1683749371, rs757139057, rs1553484094, rs747861275, rs765263671, rs1349732291, rs1017750255, rs1311042980, rs753517219	RCV001536104 RCV002488202 RCV002492327 RCV002497908 RCV004577005 RCV002226876 RCV002289374 RCV000003682 RCV000003684 RCV000003685 RCV005412478 RCV004594672 RCV003153060 RCV000369766 RCV002494861 RCV005030045 RCV005021980 RCV004577594 RCV005014767 RCV005014801 RCV004545950 RCV005015188 RCV005023573 RCV000503438 RCV000003683 RCV002507229 RCV002493328 RCV005027910 RCV002497439 RCV002505566	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NPHP1-related disorder	Pathogenic; Likely pathogenic	rs547352656, rs1458494785, rs121907899, rs2467403268, rs1017750255	RCV004734126 RCV004538648 RCV000778560 RCV004579619 RCV004535842	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Ovarian serous cystadenocarcinoma	Pathogenic	rs121907899	RCV005887256	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic	rs121907899	RCV004814818	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Senior-Loken syndrome 1	Pathogenic; Likely pathogenic	rs547352656, rs1410236296, rs773781058, rs745806504, rs1233478832, rs121907899, rs367600757, rs1388373598, rs766524637, rs376974221, rs1435671751, rs2467599617, rs2467370270, rs2467403268, rs1683749371, rs757139057, rs765263671, rs1349732291, rs1017750255, rs1311042980, rs753517219	RCV001536104 RCV002488202 RCV002492327 RCV002497908 RCV005016232 RCV005025001 RCV005412478 RCV005021662 RCV005025422 RCV002494861 RCV005030045 RCV005021980 RCV005014767 RCV005014801 RCV005015188 RCV005023573 RCV002507229 RCV002493328 RCV005027910 RCV002497439 RCV002505566	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Thyroid cancer, nonmedullary, 1	Likely pathogenic	rs2467251817	RCV005939488	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
APPENDICITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARDET-BIEDL SYNDROME	—	Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bardet-Biedl syndrome 1	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CAKUT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL APLASIA OF THE VERMIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Focal segmental glomerulosclerosis	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability, X-linked 102	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Joubert syndrome	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Joubert syndrome 1	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JOUBERT SYNDROME 4	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUVENILE NEPHRONOPHTHISIS	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KIDNEY DISEASES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leber congenital amaurosis	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Lung cancer	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEPHRONOPHTHISIS, FAMILIAL JUVENILE	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROTIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Renal dysplasia and retinal aplasia	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENIOR LOKEN SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENIOR-LOKEN SYNDROME	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Age related macular degeneration	Age-related macular degeneration	BEFREE	20981449		★☆☆☆☆ Found in Text Mining only
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Alport Syndrome	Alport Syndrome	BEFREE	31576025		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	22710270	Associate	★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Apraxia oculomotor Cogan type	Apraxia	Pubtator	37131188	Associate	★☆☆☆☆ Found in Text Mining only
Arteriosclerosis	Arteriosclerosis	BEFREE	29949740		★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	28254236	Associate	★☆☆☆☆ Found in Text Mining only
Bardet-Biedl Syndrome	Bardet-Biedl Syndrome	BEFREE	24746959, 28624958		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bardet-Biedl Syndrome	Bardet-Biedl Syndrome	ORPHANET_DG	24746959		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bardet-Biedl syndrome	Bardet-Biedl Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Brain Stem Neoplasms	Brain stem neoplasms	Pubtator	17160906	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cholestasis	Cholelithiasis	Pubtator	36227438	Associate	★☆☆☆☆ Found in Text Mining only
Chronic kidney disease stage 5	Kidney Disease	BEFREE	31096956, 31345020, 8995741		★☆☆☆☆ Found in Text Mining only
Chronic kidney disease stage 5	Kidney Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	BEFREE	17513324, 19118152, 24746959		★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathy	Pubtator	21068128, 21357692, 21866095, 22982934, 27491411, 28596487, 29146700, 35764379, 36227438	Associate	★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Congenital Abnormalities	Congenital abnormalities	Pubtator	28347285	Associate	★☆☆☆☆ Found in Text Mining only
Congenital cerebral hernia	Congenital Cerebral Hernia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of ovary	Hypoplasia of the ovary	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cystic Kidney Diseases	Cystic Kidney Disease	BEFREE	19118152, 20179356		★☆☆☆☆ Found in Text Mining only
Dandy-Walker Syndrome	Dandy-Walker Syndrome	BEFREE	10511339		★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Familial aplasia of the vermis	Cerebellar vermis agenesis	BEFREE	10511339, 15138899, 15467982, 16240161, 17409309, 17603801, 17960139, 23532844, 23683649, 24746959, 30055837		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fibrosis, Liver	Liver Fibrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Focal glomerulosclerosis	Glomerulosclerosis	BEFREE	21658830		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glycosuria Renal	Renal glycosuria	Pubtator	10712196	Associate	★☆☆☆☆ Found in Text Mining only
Gross motor development delay	Developmental delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hepatic Fibrosis, Congenital	Congenital Hepatic Fibrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydatidiform Mole	Hydatidiform mole	Pubtator	16900087	Associate	★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus Normal Pressure	Normal pressure hydrocephalus	Pubtator	11168925	Associate	★☆☆☆☆ Found in Text Mining only
Hydrocephalus, Normal Pressure	Hydrocephalus	BEFREE	10966501, 11274269, 12832729, 16155189, 18607645, 29654215, 7806215, 8995741, 9479500, 9502560, 9587065		★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★☆☆☆☆ Found in Text Mining only
Infertility Male	Male infertility	Pubtator	26198798	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	17601928		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	28254236	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Jacobsen Distal 11q Deletion Syndrome	Jacobsen Syndrome	BEFREE	18054307		★☆☆☆☆ Found in Text Mining only
Johanson-Blizzard syndrome	Johanson-Blizzard Syndrome	BEFREE	18054307		★☆☆☆☆ Found in Text Mining only
Joubert syndrome 4	Joubert syndrome	Pubtator	37131188	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JOUBERT SYNDROME 4 (disorder)	Joubert syndrome	GENOMICS_ENGLAND_DG	15689444, 22982934, 266900, 9382140		★☆☆☆☆ Found in Text Mining only
JOUBERT SYNDROME 4 (disorder)	Joubert syndrome	ORPHANET_DG	20615230		★☆☆☆☆ Found in Text Mining only
JOUBERT SYNDROME 4 (disorder)	Joubert syndrome	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Joubert syndrome with renal defect	Joubert Syndrome With Renal Defect	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Juvenile nephronophthisis	Nephronophthisis	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney Diseases	Kidney disease	Pubtator	16155189, 27004562, 36227438, 37203120	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney Diseases	Kidney Disease	BEFREE	8825638		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney Diseases	Kidney Disease	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney Diseases Cystic	Kidney disease	Pubtator	22701722, 26198798, 35676033	Associate	★☆☆☆☆ Found in Text Mining only
Kidney Failure	Kidney Failure	BEFREE	16885411, 8995741		★☆☆☆☆ Found in Text Mining only
Kidney Failure Chronic	Kidney failure	Pubtator	11168925, 21258817, 26198798, 29146700, 29654215, 31096956, 32306954, 35676033, 37296294	Associate	★☆☆☆☆ Found in Text Mining only
Kidney Failure, Chronic	Kidney Failure	BEFREE	31096956, 31345020, 8995741		★☆☆☆☆ Found in Text Mining only
Leukemia Hairy Cell	Hairy cell leukemia	Pubtator	32132867	Associate	★☆☆☆☆ Found in Text Mining only
Liver Failure	Liver failure	Pubtator	28254236	Associate	★☆☆☆☆ Found in Text Mining only
Macular Degeneration	Macular degeneration	Pubtator	20981449	Associate	★☆☆☆☆ Found in Text Mining only
Meckel syndrome type 1	Meckel Syndrome	BEFREE	17603801, 22983010		★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	BEFREE	17601928		★☆☆☆☆ Found in Text Mining only
Multicystic Dysplastic Kidney	Multicystic renal dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nephroblastoma	Nephroblastoma	BEFREE	31421145		★☆☆☆☆ Found in Text Mining only
Nephronophthisis	Nephronophthisis	BEFREE	10511339, 10712196, 10839884, 10980528, 11096053, 11261687, 11274269, 11382680, 12244321, 12536190, 12872122, 15138899, 16240161, 16522655, 16885411, 17061121, 17160906, 17409309, 17513324, 17617513, 17855640, 17960139, 21258817, 21565611, 23188109, 23683649, 25401970, 25851290, 29949740, 30087219, 30609410, 31096956, 31345020, 7806215, 8825638, 8995741, 9479500, 9794556		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis	Nephronophthisis	GENOMICS_ENGLAND_DG	15689444, 22982934		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis	Nephronophthisis	CLINVAR_DG	16762963, 18076122		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis	Nephronophthisis	HPO_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis 1	Nephronophthisis	BEFREE	10511339, 10712196, 10839884, 10980528, 11168925, 11261687, 11274269, 11382680, 15138899, 16900087, 17160906, 23683649, 26037636, 26641089, 7806215, 8697815, 8825638		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis 1	Nephronophthisis	UNIPROT_DG	10839884		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis 1	Nephronophthisis	GENOMICS_ENGLAND_DG	15689444, 22982934, 266900, 9382140		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis 1	Nephronophthisis	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephronophthisis 1	Nephronophthisis	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NEPHRONOPHTHISIS 2	Nephronophthisis	BEFREE	12872123		★☆☆☆☆ Found in Text Mining only
Nephronophthisis 2	Nephronophthisis	Pubtator	21866095, 25851290, 37203120	Associate	★☆☆☆☆ Found in Text Mining only
Nephronophthisis 3	Nephronophthisis	Pubtator	31922211	Associate	★☆☆☆☆ Found in Text Mining only
Nephronophthisis familial juvenile	Nephronophthisis	Pubtator	10712196, 11168925, 15138899, 15467982, 15786477, 16155189, 16900087, 17160906, 17617513, 18076122, 21258817, 21357692, 22701722, 22982934, 25851290, 26198798, 27004562, 27491411, 29146700, 29654215, 29949740, 30087219, 31096956, 32306954, 32361464, 33306870, 34246230, 35676033, 37203120, 37230223	Associate	★☆☆☆☆ Found in Text Mining only
Nephronophthisis familial juvenile	Nephronophthisis	Pubtator	21866095	Stimulate	★☆☆☆☆ Found in Text Mining only
Nephronophthisis, familial juvenile	Nephronophthisis	BEFREE	10511339, 10839884, 10980528, 15138899, 17160906, 23683649		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nephronophthisis, familial juvenile	Nephronophthisis	ORPHANET_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nephrosis congenital	Nephrotic syndrome	Pubtator	27004562	Associate	★☆☆☆☆ Found in Text Mining only
Nephrosis, congenital	Nephrosis, Congenital	BEFREE	27004562		★☆☆☆☆ Found in Text Mining only
Nephrotic Syndrome	Nephrotic Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculomotor apraxia	Oculomotor apraxia	BEFREE	10839884		★☆☆☆☆ Found in Text Mining only
Oculomotor apraxia	Oculomotor apraxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculovestibuloauditory syndrome	Oculovestibuloauditory Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polyendocrinopathies, Autoimmune	Autoimmune Polyendocrinopathy	BEFREE	19350199		★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Premature Menopause	Premature Menopause	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Renal corticomedullary cysts	Renal corticomedullary cysts	HPO_DG			★☆☆☆☆ Found in Text Mining only
Renal dysplasia and retinal aplasia (disorder)	Renal dysplasia and retinal aplasia	GENOMICS_ENGLAND_DG	15689444, 22982934		★☆☆☆☆ Found in Text Mining only
Renal dysplasia and retinal aplasia (disorder)	Renal dysplasia and retinal aplasia	ORPHANET_DG	22819833		★☆☆☆☆ Found in Text Mining only
Renal dysplasia and retinal aplasia (disorder)	Renal dysplasia and retinal aplasia	BEFREE	24674142		★☆☆☆☆ Found in Text Mining only
Renal dysplasia and retinal aplasia (disorder)	Renal dysplasia and retinal aplasia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Renal Insufficiency	Renal Insufficiency	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	40725491	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	HPO_DG			★☆☆☆☆ Found in Text Mining only
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Senior Loken Syndrome	Senior-loken syndrome	Pubtator	37296294, 40725491	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Senior-Loken syndrome	Senior-Loken Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Senior-Loken Syndrome 1	Senior-Loken Syndrome	GENOMICS_ENGLAND_DG	22982934, 266900, 9382140		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Senior-Loken Syndrome 1	Senior-Loken Syndrome	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Speech Disorders	Speech Disorders	HPO_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Syndactyly of fingers	Syndactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ulnar polydactyly of fingers	Postaxial hand polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Vision Disorders	Visual disorder	Pubtator	40725491	Associate	★☆☆☆☆ Found in Text Mining only