PDZD7 PDZ domain containing 7 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDZD7provided by HGNC
Official Full Name: PDZ domain containing 7provided by HGNC
Primary source: HGNC:HGNC:26257
See related: Ensembl:ENSG00000186862 MIM:612971; AllianceGenome:HGNC:26257
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PDZK7; DFNB57
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 different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]
Expression: Broad expression in small intestine (RPKM 3.0), duodenum (RPKM 1.7) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q24.31

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (101007679..101031129, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (101891054..101914544, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (102767436..102790886, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical characterizations and molecular genetic study of two co-segregating variants in PDZD7 and PDE6C genes leading simultaneously to non-syndromic hearing loss and achromatopsia.
Title: Clinical characterizations and molecular genetic study of two co-segregating variants in PDZD7 and PDE6C genes leading simultaneously to non-syndromic hearing loss and achromatopsia.
Novel homozygous variant in the PDZD7 gene in a family with nonsyndromic sensorineural hearing loss.
Title: Novel homozygous variant in the PDZD7 gene in a family with nonsyndromic sensorineural hearing loss.
PDZD7 can be an important causative gene for moderate to severe ARNSHL in Koreans. Moreover, at least some, if not all, p.Arg164Trp alleles in Koreans could exert a potential founder effect and arise from diverse haplotypes as a mutational hot spot.
Title: Identification of a Potential Founder Effect of a Novel PDZD7 Variant Involved in Moderate-to-Severe Sensorineural Hearing Loss in Koreans.
Three mutations in PDZD7 gene linked to autosomal recessive non-syndromic hearing loss (ARNSHL) were identified in a Chinese pedigree. The findings expand not only our knowledge of genetic causes of ARNSHL, but also PDZD7 genes mutation spectrum of the disease. They will aid personalized genetic counseling, molecular diagnostics and clinical management of this condition.
Title: Novel recessive PDZD7 biallelic mutations associated with hereditary hearing loss in a Chinese pedigree.
Lnc-PDZD7 promotes stemness properties and suppresses chemosensitivity though the miR-101/EZH2/ATOH8 pathway.
Title: Lnc-PDZD7 contributes to stemness properties and chemosensitivity in hepatocellular carcinoma through EZH2-mediated ATOH8 transcriptional repression.
This is the first report to identify PDZD7 as an ARNSHL-associated gene in the Chinese population. Our finding could expand the pathogenic spectrum and strengthens the clinical diagnostic role of the PDZD7 gene in ARNSHL patients.
Title: Novel recessive PDZD7 biallelic mutations in two Chinese families with non-syndromic hearing loss.
PDZD7 is confirmed as a bona fide autosomal recessive nonsyndromic hearing loss gene.
Title: Confirmation of PDZD7 as a Nonsyndromic Hearing Loss Gene.
Mutations in PDZD7 cause autosomal recessive non-syndromic hearing loss.
Title: PDZD7 and hearing loss: More than just a modifier.
Both WHRN and PDZD7 are required for the complex formation with USH2A and GPR98.
Title: Whirlin and PDZ domain-containing 7 (PDZD7) proteins are both required to form the quaternary protein complex associated with Usher syndrome type 2.
overexpression of another Usher syndrome protein, PDZD7, decreased the AC inhibition of the VLGR1 beta-subunit
Title: Constitutive Gαi coupling activity of very large G protein-coupled receptor 1 (VLGR1) and its regulation by PDZD7 protein.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hearing loss, autosomal recessive 57 MedGen: C4693893 OMIM: 618003 GeneReviews: Not available	Compare labs
Usher syndrome type 2A MedGen: C1848634 OMIM: 276901 GeneReviews: Usher Syndrome Type II	Compare labs
Usher syndrome type 2C MedGen: C2931213 OMIM: 605472 GeneReviews: Usher Syndrome Type II	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

D11S3114 (e-PCR)
- UniSTS:152207

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within auditory receptor cell development	ISS Inferred from Sequence or Structural Similarity more info
involved_in auditory receptor cell stereocilium organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within auditory receptor cell stereocilium organization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of sound	ISS Inferred from Sequence or Structural Similarity more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within establishment of protein localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in inner ear receptor cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in sensory perception of sound	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of USH2 complex	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in stereocilia ankle link	ISS Inferred from Sequence or Structural Similarity more info
part_of stereocilia ankle link complex	IBA Inferred from Biological aspect of Ancestor more info
part_of stereocilia ankle link complex	ISS Inferred from Sequence or Structural Similarity more info
located_in stereocilium	ISS Inferred from Sequence or Structural Similarity more info
is_active_in stereocilium tip	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: PDZ domain-containing protein 7

Names: deafness, autosomal recessive 57

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_028030.1 RefSeqGene

Range

5029..28479

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001195263.2 → NP_001182192.1 PDZ domain-containing protein 7 isoform 1

See identical proteins and their annotated locations for NP_001182192.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AK026862, AL133215, DA197280, FJ617449

Consensus CDS

CCDS73182.1

UniProtKB/Swiss-Prot

D5FJ77, Q8N321, Q9H5P4

Related

ENSP00000480489.1, ENST00000619208.6

Conserved Domains (2) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd07358
Location:554 → 630

HN_PDZD7_like; harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins
NM_001351044.2 → NP_001337973.1 PDZ domain-containing protein 7 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the coding region, which results in a frameshift, lacks multiple exons in the 3' coding region, and has a distinct 3' terminal exon, resulting in a distinct 3' coding region and 3' UTR compared to variant 1. It encodes isoform 3, which has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK026862, AL133215, AW058493, DA197280, FJ617449

Conserved Domains (1) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
NM_024895.5 → NP_079171.1 PDZ domain-containing protein 7 isoform 2

See identical proteins and their annotated locations for NP_079171.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1 and is also known as PDZD7-A.

Source sequence(s)

AK026862, AL133215, DA197280

Consensus CDS

CCDS31269.1

UniProtKB/Swiss-Prot

Q9H5P4

Related

ENSP00000359234.3, ENST00000370215.7

Conserved Domains (1) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

101007679..101031129 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011540178.4 → XP_011538480.1 PDZ domain-containing protein 7 isoform X2

Conserved Domains (2) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd07358
Location:553 → 629

HN_PDZD7_like; harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins
XM_011540177.4 → XP_011538479.1 PDZ domain-containing protein 7 isoform X1

See identical proteins and their annotated locations for XP_011538479.1

UniProtKB/Swiss-Prot

D5FJ77, Q8N321, Q9H5P4

Conserved Domains (2) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd07358
Location:554 → 630

HN_PDZD7_like; harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins
XM_047425767.1 → XP_047281723.1 PDZ domain-containing protein 7 isoform X1

UniProtKB/Swiss-Prot

D5FJ77, Q8N321, Q9H5P4
XM_011540179.4 → XP_011538481.1 PDZ domain-containing protein 7 isoform X4

Conserved Domains (2) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd07358
Location:554 → 630

HN_PDZD7_like; harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins
XM_047425768.1 → XP_047281724.1 PDZ domain-containing protein 7 isoform X3
XM_005270165.4 → XP_005270222.1 PDZ domain-containing protein 7 isoform X6

UniProtKB/TrEMBL

A0A2R8Y892

Related

ENSP00000496747.1, ENST00000644782.1

Conserved Domains (1) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
XM_011540181.4 → XP_011538483.1 PDZ domain-containing protein 7 isoform X7

Conserved Domains (1) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
XM_011540183.4 → XP_011538485.1 PDZ domain-containing protein 7 isoform X8

Conserved Domains (1) summary

cd00992
Location:84 → 164

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
XM_017016667.3 → XP_016872156.1 PDZ domain-containing protein 7 isoform X5

UniProtKB/TrEMBL

A0A2R8YFN1

Related

ENSP00000495283.1, ENST00000645349.1
XM_017016668.3 → XP_016872157.1 PDZ domain-containing protein 7 isoform X9
XM_047425769.1 → XP_047281725.1 PDZ domain-containing protein 7 isoform X5

UniProtKB/TrEMBL

A0A2R8YFN1
XM_047425771.1 → XP_047281727.1 PDZ domain-containing protein 7 isoform X10

RNA

XR_945816.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060934.1 Alternate T2T-CHM13v2.0

Range

101891054..101914544 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054366764.1 → XP_054222739.1 PDZ domain-containing protein 7 isoform X1

UniProtKB/Swiss-Prot

D5FJ77, Q8N321, Q9H5P4
XM_054366765.1 → XP_054222740.1 PDZ domain-containing protein 7 isoform X2
XM_054366763.1 → XP_054222738.1 PDZ domain-containing protein 7 isoform X1

UniProtKB/Swiss-Prot

D5FJ77, Q8N321, Q9H5P4
XM_054366766.1 → XP_054222741.1 PDZ domain-containing protein 7 isoform X4
XM_054366769.1 → XP_054222744.1 PDZ domain-containing protein 7 isoform X6

UniProtKB/TrEMBL

A0A2R8Y892
XM_054366770.1 → XP_054222745.1 PDZ domain-containing protein 7 isoform X7
XM_054366771.1 → XP_054222746.1 PDZ domain-containing protein 7 isoform X8
XM_054366767.1 → XP_054222742.1 PDZ domain-containing protein 7 isoform X5

UniProtKB/TrEMBL

A0A2R8YFN1
XM_054366772.1 → XP_054222747.1 PDZ domain-containing protein 7 isoform X9
XM_054366768.1 → XP_054222743.1 PDZ domain-containing protein 7 isoform X5

UniProtKB/TrEMBL

A0A2R8YFN1
XM_054366773.1 → XP_054222748.1 PDZ domain-containing protein 7 isoform X10