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    PKHD1L1 PKHD1 like 1 [ Homo sapiens (human) ]

    Gene ID: 93035, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PKHD1L1provided by HGNC
    Official Full Name
    PKHD1 like 1provided by HGNC
    Primary source
    HGNC:HGNC:20313
    See related
    Ensembl:ENSG00000205038 MIM:607843; AllianceGenome:HGNC:20313
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PKHDL1; DFNB124
    Summary
    Predicted to act upstream of or within sensory perception of sound. Predicted to be located in cytosol. Implicated in autosomal recessive nonsyndromic deafness. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in thyroid (RPKM 10.5) and lymph node (RPKM 0.8) See more
    Orthologs
    mouse all
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    Genomic context

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    See PKHD1L1 in Genome Data Viewer
    Location:
    8q23.1-q23.2
    Exon count:
    79
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (109362461..109537207)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (110491005..110665782)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (110374690..110549436)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:110274967-110275602 Neighboring gene NudC domain containing 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:110332106-110332753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27805 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:110346420-110347342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19469 Neighboring gene ENY2 transcription and export complex 2 subunit Neighboring gene suppressor of cytokine signaling 5 pseudogene Neighboring gene mitogen-activated protein kinase 6 pseudogene 5 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:110534343-110535542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27809 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27811 Neighboring gene estrogen receptor binding site associated antigen 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27812 Neighboring gene NANOG hESC enhancer GRCh37_chr8:110625919-110626714 Neighboring gene syntabulin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:110656818-110657754 Neighboring gene SYBU antisense RNA 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss. Redfield SE, et al. Hum Genet, 2024 Mar. PMID 38459354, Free PMC Article
    2. Systematic Multiomic Analysis of PKHD1L1 Gene Expression and Its Role as a Predicting Biomarker for Immune Cell Infiltration in Skin Cutaneous Melanoma and Lung Adenocarcinoma. Kang JY, et al. Int J Mol Sci, 2023 Dec 26. PMID 38203530, Free PMC Article
    3. [Preparation and characterization of a polyclonal antibody against human Fibrocystin-L]. Lian PW, et al. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, 2011 Jan. PMID 21208571
    4. [Role of PLAT, PKHD1L1, STK38L and TEAD1 genes Alu-polymorphism for longevity]. Erdman VV, et al. Adv Gerontol, 2016. PMID 28556638
    5. PKHDL1, a homolog of the autosomal recessive polycystic kidney disease gene, encodes a receptor with inducible T lymphocyte expression. Hogan MC, et al. Hum Mol Genet, 2003 Mar 15. PMID 12620974

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss.
      Title: PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss.
    2. Systematic Multiomic Analysis of PKHD1L1 Gene Expression and Its Role as a Predicting Biomarker for Immune Cell Infiltration in Skin Cutaneous Melanoma and Lung Adenocarcinoma.
      Title: Systematic Multiomic Analysis of PKHD1L1 Gene Expression and Its Role as a Predicting Biomarker for Immune Cell Infiltration in Skin Cutaneous Melanoma and Lung Adenocarcinoma.
    3. High probability of detection of PKHD1L1*I/I had a Long-lived women and PKHD1L1*I/D genotype was a significant factor in providing of male longevity of the ethnically homogeneous group of Tatars from the Republic of Bashkortostan, Russia.
      Title: [Role of PLAT, PKHD1L1, STK38L and TEAD1 genes Alu-polymorphism for longevity].
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. PKHDL1 may have a role in cellular immunity
      Title: PKHDL1, a homolog of the autosomal recessive polycystic kidney disease gene, encodes a receptor with inducible T lymphocyte expression.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp586C1021

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables signaling receptor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in immune response NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in extracellular space NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in stereocilium coat IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in stereocilium membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in stereocilium tip IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    fibrocystin-L
    Names
    PKHD1-like protein 1
    polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1
    polycystic kidney and hepatic disease 1-like protein 1
    polycystic kidney and hepatic disease-like 1

    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.

    mRNA and Protein(s)

    1. NM_177531.6 → NP_803875.2  fibrocystin-L precursor

      See identical proteins and their annotated locations for NP_803875.2

      Status: VALIDATED

      Source sequence(s)
      AC021001, AC021237, AI923283, AP000427
      Consensus CDS
      CCDS47911.1
      UniProtKB/Swiss-Prot
      Q567P2, Q86WI1, Q9UF27
      Related
      ENSP00000367655.5, ENST00000378402.10
      Conserved Domains (6) summary
      cd00603
      Location:271 → 363
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      cd04217
      Location:1395 → 1498
      Cupredoxin_Fibrocystin-L_like; Cupredoxin domain of PKHDL1, a homolog of the autosomal recessive polycystic kidney disease protein
      pfam01833
      Location:1916 → 1997
      TIG; IPT/TIG domain
      pfam10162
      Location:2185 → 2303
      G8; G8 domain
      pfam13229
      Location:3328 → 3501
      Beta_helix; Right handed beta helix region
      cl08459
      Location:363 → 467
      PA14; PA14 domain

    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

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      109362461..109537207
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011517371.3 → XP_011515673.1  fibrocystin-L isoform X1

      Conserved Domains (6) summary
      cd00603
      Location:271 → 363
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      cd04217
      Location:1395 → 1498
      Cupredoxin_Fibrocystin-L_like; Cupredoxin domain of PKHDL1, a homolog of the autosomal recessive polycystic kidney disease protein
      pfam01833
      Location:1916 → 1997
      TIG; IPT/TIG domain
      pfam10162
      Location:2185 → 2303
      G8; G8 domain
      pfam13229
      Location:3328 → 3501
      Beta_helix; Right handed beta helix region
      cl08459
      Location:363 → 467
      PA14; PA14 domain

    2. XM_017013971.2 → XP_016869460.2  fibrocystin-L isoform X3

    3. XM_047422421.1 → XP_047278377.1  fibrocystin-L isoform X4

    4. XM_047422420.1 → XP_047278376.1  fibrocystin-L isoform X2

    5. XM_047422422.1 → XP_047278378.1  fibrocystin-L isoform X5

    6. XM_017013974.2 → XP_016869463.2  fibrocystin-L isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      110491005..110665782
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361509.1 → XP_054217484.1  fibrocystin-L isoform X3

    2. XM_054361510.1 → XP_054217485.1  fibrocystin-L isoform X4

    3. XM_054361508.1 → XP_054217483.1  fibrocystin-L isoform X2

    4. XM_054361507.1 → XP_054217482.1  fibrocystin-L isoform X1

    5. XM_054361511.1 → XP_054217486.1  fibrocystin-L isoform X5

    6. XM_054361512.1 → XP_054217487.1  fibrocystin-L isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86WI1.2 GenPept UniProtKB/Swiss-Prot:Q86WI1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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