PDZD7 (PDZ domain containing 7)

Gene

• Entrez ID: 79955
• Gene name: PDZ domain containing 7
• Gene symbol: PDZD7
• Synonyms (NCBI Gene): DFNB57, PDZK7
• Chromosome: 10
• Chromosome location: 10q24.31
• Summary: This gene encodes a ciliary protein homologous to proteins which are mutated in Usher syndrome patients, and mutations and translocations involving this gene have been associated with two types of Usher syndrome. Multiple transcript variants encoding diff

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs118098246	A>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, non coding transcript variant, coding sequence variant
rs148695069	C>A,G,T	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs397516633	T>-	Likely-pathogenic, pathogenic	Frameshift variant, downstream transcript variant, coding sequence variant, genic downstream transcript variant, 3 prime UTR variant
rs753034799	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs953422571	G>A,T	Likely-pathogenic	Non coding transcript variant, missense variant, synonymous variant, coding sequence variant, stop gained
rs1554834161	G>A	Pathogenic	Downstream transcript variant, intron variant, stop gained, 3 prime UTR variant, coding sequence variant, genic downstream transcript variant
rs1554834186	G>A	Pathogenic	Intron variant, non coding transcript variant, stop gained, 3 prime UTR variant, coding sequence variant, genic downstream transcript variant
rs1554835103	G>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1554835827	A>C	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1564634581	T>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1590045340	G>-	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant, downstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1224072	hsa-miR-1182	CLIP-seq
MIRT1224073	hsa-miR-1303	CLIP-seq
MIRT1224074	hsa-miR-193a-5p	CLIP-seq
MIRT1224075	hsa-miR-431	CLIP-seq
MIRT1224076	hsa-miR-4423-5p	CLIP-seq
MIRT1224077	hsa-miR-4781-3p	CLIP-seq
MIRT2065319	hsa-miR-2110	CLIP-seq
MIRT2065320	hsa-miR-3134	CLIP-seq
MIRT2065321	hsa-miR-3150a-3p	CLIP-seq
MIRT2065322	hsa-miR-3175	CLIP-seq
MIRT2065323	hsa-miR-4534	CLIP-seq
MIRT2065324	hsa-miR-939	CLIP-seq
MIRT1224072	hsa-miR-1182	CLIP-seq
MIRT1224074	hsa-miR-193a-5p	CLIP-seq
MIRT2293153	hsa-miR-3122	CLIP-seq
MIRT2293154	hsa-miR-3663-5p	CLIP-seq
MIRT2293155	hsa-miR-3689a-3p	CLIP-seq
MIRT2293156	hsa-miR-3689c	CLIP-seq
MIRT2293157	hsa-miR-3913-5p	CLIP-seq
MIRT1224075	hsa-miR-431	CLIP-seq
MIRT1224076	hsa-miR-4423-5p	CLIP-seq
MIRT1224077	hsa-miR-4781-3p	CLIP-seq
MIRT2293158	hsa-miR-500a	CLIP-seq
MIRT2065319	hsa-miR-2110	CLIP-seq
MIRT2065321	hsa-miR-3150a-3p	CLIP-seq
MIRT2065322	hsa-miR-3175	CLIP-seq
MIRT2065324	hsa-miR-939	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002141	Component	Stereocilia ankle link	IEA
GO:0002141	Component	Stereocilia ankle link	ISS
GO:0002142	Component	Stereocilia ankle link complex	IBA
GO:0002142	Component	Stereocilia ankle link complex	IEA
GO:0002142	Component	Stereocilia ankle link complex	ISS
GO:0005515	Function	Protein binding	IPI	19028668, 20440071
GO:0005615	Component	Extracellular space	HDA	22664934
GO:0005634	Component	Nucleus	IDA	20440071
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005886	Component	Plasma membrane	IBA
GO:0005929	Component	Cilium	IBA
GO:0005929	Component	Cilium	IDA	20440071
GO:0005929	Component	Cilium	IEA
GO:0007605	Process	Sensory perception of sound	IBA
GO:0032420	Component	Stereocilium	IEA
GO:0032420	Component	Stereocilium	ISS
GO:0032426	Component	Stereocilium tip	IBA
GO:0036064	Component	Ciliary basal body	IDA
GO:0042802	Function	Identical protein binding	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043226	Component	Organelle	IEA
GO:0045184	Process	Establishment of protein localization	IEA
GO:0045184	Process	Establishment of protein localization	ISS
GO:0050910	Process	Detection of mechanical stimulus involved in sensory perception of sound	IEA
GO:0050910	Process	Detection of mechanical stimulus involved in sensory perception of sound	ISS
GO:0051649	Process	Establishment of localization in cell	IEA
GO:0060088	Process	Auditory receptor cell stereocilium organization	IBA
GO:0060088	Process	Auditory receptor cell stereocilium organization	IEA
GO:0060088	Process	Auditory receptor cell stereocilium organization	ISS
GO:0060113	Process	Inner ear receptor cell differentiation	NAS	25406310
GO:0060117	Process	Auditory receptor cell development	IEA
GO:0060117	Process	Auditory receptor cell development	ISS
GO:0120025	Component	Plasma membrane bounded cell projection	IEA
GO:1990696	Component	USH2 complex	IEA
GO:1990696	Component	USH2 complex	ISS

Other IDs

• MIM: 612971
• HGNC: 26257
• e!Ensembl: ENSG00000186862

Protein

• UniProt ID: Q9H5P4
• Protein name: PDZ domain-containing protein 7
• Protein function: In cochlear developing hair cells, essential in organizing the USH2 complex at stereocilia ankle links. Blocks inhibition of adenylate cyclase activity mediated by ADGRV1.
• PDB: 2EEH, 7PC5
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00595	PDZ	86 → 164	PDZ domain	Domain
  PF00595	PDZ	212 → 289	PDZ domain	Domain
  PF00595	PDZ	862 → 947	PDZ domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Weakly expressed in the inner ear. Expressed in the retinal pigment epithelium. {ECO:0000269|PubMed:19028668, ECO:0000269|PubMed:20440071}.
• Sequence:

  MAQGFAVGFDPLGLGDLSSGSLSSLSSRGHLGSDSGSTATRYLLRKQQRLLNGPPRGIRA
  SSPMGRVILINSPIEANSDESDIIHSVRVEKSPAGRLGFSVRGGSEHGLGIFVSKVEEGS
  SAERAGLCVGDKITEVNGLSLESTTMGSAVKVLTSSSRLHMMVRRMGRVPGIKFSKEKTT
  WVDVVNRRLVVEKCGSTPSDTSSEDGVRRIVHLYTTSDDFCLGFNIRGGKEFGLGIYVSK
  VDHGGLAEENGIKVGDQVLAANGVRFDDISHSQAVEVLKGQTHIMLTIKETGRYPAYKEM
  VSEYCWLDRLSNGVLQQLSPASESSSSVSSCASSAPYSSGSLPSDRMDICLGQEEPGSRG
  PGWGRADTAMQTEPDAGGRVETWCSVRPTVILRDTAIRSDGPHPGRRLDSALSESPKTAL
  LLALSRPRPPITRSQSYLTLWEEKQQRKKEKSGSPGEKGALQRSKTLMNLFFKGGRQGRL
  ARDGRREAWTLDSGSLAKTYPRLDIEKAGGVGPVQKFVTWRLRRDQERGRALLSARSGSP
  SSQLPNVDEQVQAWESRRPLIQDLAQRLLTDDEVLAVTRHCSRYVHEGGIEDLVRPLLAI
  LDRPEKLLLLQDIRSVVAPTDLGRFDSMVMLVELEAFEALKSRAVRPPALRPARQDTPPK
  RHLITPVPDSRGGFYLLPVNGFPEEEDNGELRERLGALKVSPSASAPRHPHKGIPPLQDV
  PVDAFTPLRIACTPPPQLPPVAPRPLRPNWLLTEPLSREHPPQSQIRGRAQSRSRSRSRS
  RSRSSRGQGKSPGRRSPSPVPTPAPSMTNGRYHKPRKARPPLPRPLDGEAAKVGAKQGPS
  ESGTEGTAKEAAMKNPSGELKTVTLSKMKQSLGISISGGIESKVQPMVKIEKIFPGGAAF
  LSGALQAGFELVAVDGENLEQVTHQRAVDTIRRAYRNKAREPMELVVRVPGPSPRPSPSD
  SSALTDGGLPADHLPAHQPLDAAPVPAHWLPEPPTNPQTPPTDARLLQPTPSPAPSPALQ
  TPDSKPAPSPRIP

• Sequence length: 1033

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
Deafness	Likely pathogenic; Pathogenic	rs2492782810	RCV004798951	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ear malformation	Likely pathogenic	rs1002525817	RCV001836910	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hearing loss, autosomal recessive	Likely pathogenic; Pathogenic	rs1157689930, rs587776894	RCV004719052 RCV004719034	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hearing loss, autosomal recessive 57	Likely pathogenic; Pathogenic	rs979094623, rs2134074165, rs778565403, rs2134088502, rs587776894, rs148695069, rs1554835827, rs953422571, rs1554834186, rs1554834161, rs1554835103, rs1055318738, rs773193491	RCV003333179 RCV005253973 RCV003155458 RCV002470580 RCV000656379 RCV000656349 RCV000656350 RCV000656351 RCV000656352 RCV000656354 RCV000656357 RCV001171317 RCV001281370	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nonsyndromic genetic hearing loss	Likely pathogenic; Pathogenic	rs1157689930	RCV004018298	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PDZD7-related disorder	Likely pathogenic; Pathogenic	rs1378470761, rs34705415, rs2493052165, rs771163176	RCV004550097 RCV003155499 RCV004550632 RCV004548732	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rare genetic deafness	Likely pathogenic	rs2492943549	RCV004018227	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher syndrome	Pathogenic	rs766167046, rs753591187	RCV003389556 RCV003389557	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher syndrome type 2A	Pathogenic	rs587776894, rs1564634581	RCV000023974 RCV000678984	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher syndrome type 2C	Likely pathogenic; Pathogenic	rs979094623, rs587776894, rs148695069	RCV003147675 RCV004760341 RCV003989572	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher syndrome, type IIC, GPR98/PDZD7 digenic	Pathogenic	rs2492782878	RCV000023975	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL EAR ANOMALY NOS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL RECESSIVE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL RECESSIVE 57	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hearing impairment	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal dystrophy	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME TYPE 2	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE 2A	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE 2C	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE IIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE IIC	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anxiety	Anxiety Disorder	HPO_DG			★☆☆☆☆ 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
Congenital sensorineural hearing loss	Congenital Sensorineural Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Deafness	Deafness	Pubtator	26416264, 32048449, 35248088	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Deafness Autosomal Recessive	Deafness	Pubtator	28173822	Associate	★☆☆☆☆ Found in Text Mining only
DEAFNESS, AUTOSOMAL RECESSIVE (disorder)	Deafness	BEFREE	19028668		★☆☆☆☆ Found in Text Mining only
DEAFNESS, AUTOSOMAL RECESSIVE (disorder)	Deafness	CLINGEN_DG	19028668, 23055499, 24334608, 25122905, 26416264, 26445815, 26849169, 27068579, 27525485, 28173822		★☆☆☆☆ Found in Text Mining only
DEAFNESS, AUTOSOMAL RECESSIVE 57	Deafness	UNIPROT_DG	19028668, 26416264, 26849169, 29048736		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL RECESSIVE 57	Deafness	CLINVAR_DG	26416264		★★☆☆☆ 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
Hallucinations	Hallucinations	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	26416264, 31454969, 35248088, 35715776	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	31454969	Associate	★☆☆☆☆ Found in Text Mining only
Hemianopsia	Hemianopsia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	30786928		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	30786928		★☆☆☆☆ Found in Text Mining only
Microdontia (disorder)	Microdontia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Nonsyndromic Deafness	BEFREE	26849169		★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	BEFREE	20440071, 26849169		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	20440071	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	20440071		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	20440071, 32050993	Associate	★☆☆☆☆ Found in Text Mining only
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	26849169		★☆☆☆☆ 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	BEFREE	19028668, 20440071, 23055499, 25404053, 26849169, 29142287		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher Syndrome	Usher Syndrome	LHGDN	19028668		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher syndrome type 1C	Usher syndrome	Pubtator	20440071	Associate	★☆☆☆☆ Found in Text Mining only
Usher syndrome type 2	Usher Syndrome	ORPHANET_DG	20440071		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher syndrome type 2	Usher Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher syndrome type 2	Usher Syndrome	BEFREE	22147658, 25406310, 31454969		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndrome Type IF	Usher syndrome	Pubtator	31454969	Associate	★☆☆☆☆ Found in Text Mining only
Usher syndrome, type 2C	Usher Syndrome	GENOMICS_ENGLAND_DG	26416264		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher syndrome, type 2C	Usher Syndrome	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndrome, Type II	Usher Syndrome	ORPHANET_DG	20440071		★☆☆☆☆ Found in Text Mining only
USHER SYNDROME, TYPE IIA	Usher Syndrome	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE IIA	Usher Syndrome	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE IIA	Usher Syndrome	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndromes	Usher syndrome	Pubtator	20440071, 25404053	Associate	★☆☆☆☆ Found in Text Mining only