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

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Deafness	Likely pathogenic; Pathogenic	rs2492782810	RCV004798951
Ear malformation	Likely pathogenic	rs1002525817	RCV001836910
Hearing loss, autosomal recessive	Likely pathogenic; Pathogenic	rs1157689930, rs587776894	RCV004719052 RCV004719034
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
Nonsyndromic genetic hearing loss	Likely pathogenic; Pathogenic	rs1157689930	RCV004018298
PDZD7-related disorder	Likely pathogenic; Pathogenic	rs1378470761, rs34705415, rs2493052165, rs771163176	RCV004550097 RCV003155499 RCV004550632 RCV004548732
Rare genetic deafness	Likely pathogenic	rs2492943549	RCV004018227
Usher syndrome	Pathogenic	rs766167046, rs753591187	RCV003389556 RCV003389557
Usher syndrome type 2A	Pathogenic	rs587776894, rs1564634581	RCV000023974 RCV000678984
Usher syndrome type 2C	Likely pathogenic; Pathogenic	rs979094623, rs587776894, rs148695069	RCV003147675 RCV004760341 RCV003989572
Usher syndrome, type IIC, GPR98/PDZD7 digenic	Pathogenic	rs2492782878	RCV000023975

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Benign	rs77802680	RCV005920134
Cervical cancer	Benign	rs77802680	RCV005920136
Cholangiocarcinoma	Benign	rs191331869	RCV005916937
Familial cancer of breast	Uncertain significance	rs368813546	RCV005910996
Gastric cancer	Benign	rs191331869	RCV005916935
Hearing impairment	Uncertain significance; Conflicting classifications of pathogenicity	rs911911177, rs2133994567, rs1170141042, rs2134047337, rs372777810, rs397516636, rs202154862, rs573956926	RCV001375315 RCV001375231 RCV001375409 RCV001375149 RCV001375232 RCV005621856 RCV001375109 RCV001375141
Malignant tumor of esophagus	Benign	rs77802680	RCV005920135
Retinal dystrophy	Uncertain significance; Conflicting classifications of pathogenicity	rs972518774, rs555444131, rs571399433, rs1241902972, rs397516633, rs202154862, rs202192219, rs549755324	RCV004815683 RCV004815245 RCV004816479 RCV004818446 RCV004814956 RCV004813628 RCV004813834 RCV004813835
Thymoma	Benign	rs77802680	RCV005920137
Uterine carcinosarcoma	Benign	rs191331869	RCV005916936
Uterine corpus endometrial carcinoma	Benign	rs77802680	RCV005920138

Associations from Text Mining
Disease Name	Relationship Type	References
Deafness	Associate	26416264, 32048449, 35248088
Deafness Autosomal Recessive	Associate	28173822
Hearing Loss	Associate	26416264, 31454969, 35248088, 35715776
Hearing Loss Sensorineural	Associate	31454969
Nonsyndromic sensorineural hearing loss	Associate	28173822, 29048736, 33530996, 35715776
Retinal Diseases	Associate	20440071
Retinitis Pigmentosa	Associate	20440071, 32050993
Usher syndrome type 1C	Associate	20440071
Usher Syndrome Type IF	Associate	31454969
Usher Syndromes	Associate	20440071, 25404053