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    KLHDC4 kelch domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 54758, updated on 27-Nov-2024

    Summary

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    Official Symbol
    KLHDC4provided by HGNC
    Official Full Name
    kelch domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:25272
    See related
    Ensembl:ENSG00000104731 MIM:620518; AllianceGenome:HGNC:25272
    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
    Expression
    Ubiquitous expression in testis (RPKM 2.9), lymph node (RPKM 1.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KLHDC4 in Genome Data Viewer
    Location:
    16q24.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (87698146..87765986, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (93769791..93838649, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (87741418..87799592, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87634653-87635215 Neighboring gene junctophilin 3 repeat instability region Neighboring gene MPRA-validated peak2658 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87648002-87648502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87653056-87653900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87653901-87654745 Neighboring gene junctophilin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11324 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:87691195-87691930 and GRCh37_chr16:87691931-87692664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87692665-87693398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87695971-87696921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87709103-87709651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87713011-87713917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87718372-87718956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87718957-87719539 Neighboring gene uncharacterized LOC100129215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11327 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:87736382-87737581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87738231-87738840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87738841-87739448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87742491-87743098 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:87750381-87750569 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:87758101-87759300 Neighboring gene uncharacterized LOC124903752 Neighboring gene uncharacterized LOC124903751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87782061-87782712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87798880-87799504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11331 Neighboring gene uncharacterized LOC105371399 Neighboring gene uncharacterized LOC102724467 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:87806571-87806776 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87811607-87812472 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87812473-87813338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87813339-87814204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11335 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:87823556-87824755 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87837714-87838214 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87839527-87840470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87840471-87841412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11340 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87856683-87857676 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87858671-87859662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87861620-87862209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87863388-87863975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:87865154-87865742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:87867637-87868191 Neighboring gene Sharpr-MPRA regulatory region 5705 Neighboring gene solute carrier family 7 member 5 Neighboring gene microRNA 6775

    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
    • 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. Upregulation of KLHDC4 Predicts a Poor Prognosis in Human Nasopharyngeal Carcinoma. Lian YF, et al. PLoS One, 2016. PMID 27030985, Free PMC Article
    2. A repeat expansion in the gene encoding junctophilin-3 is associated with Huntington disease-like 2. Holmes SE, et al. Nat Genet, 2001 Dec. PMID 11694876
    3. Huntington Disease-Like 2. Adam MP, et al. , 1993. PMID 20301701
    4. Hereditary Dystonia Overview. Adam MP, et al. , 1993. PMID 20301334
    5. The E3 ubiquitin ligase UBR5 interacts with the H/ACA ribonucleoprotein complex and regulates ribosomal RNA biogenesis in embryonic stem cells. Saez I, et al. FEBS Lett, 2020 Jan. PMID 31365120

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. KLHDC4 promotes NPC oncogenesis by suppressing cellular apoptosis.
      Title: Upregulation of KLHDC4 Predicts a Poor Prognosis in Human Nasopharyngeal Carcinoma.
    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

    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

    Homology

    Clone Names

    • FLJ00104, FLJ35576, FLJ45755, DKFZp434G0522

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    kelch domain-containing protein 4

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001184854.2 → NP_001171783.1  kelch domain-containing protein 4 isoform 3

      See identical proteins and their annotated locations for NP_001171783.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons in the coding region and uses an alternate splice site in the 3' UTR compared to variant 1. The resulting protein (isoform 3) is shorter but has the same N- and C-terminus compared to isoform 1.
      Source sequence(s)
      BC001044, BC022969, BP215584
      Consensus CDS
      CCDS54050.1
      UniProtKB/TrEMBL
      Q9H863
      Related
      ENSP00000262530.5, ENST00000353170.9
      Conserved Domains (3) summary
      sd00038
      Location:62 → 117
      Kelch; KELCH repeat [structural motif]
      pfam13415
      Location:129 → 181
      Kelch_3; Galactose oxidase, central domain
      pfam13418
      Location:173 → 229
      Kelch_4; Galactose oxidase, central domain

    2. NM_001184856.2 → NP_001171785.1  kelch domain-containing protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001171785.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-terminus compared to isoform 1.
      Source sequence(s)
      BC011680, BP215584
      Consensus CDS
      CCDS54051.1
      UniProtKB/TrEMBL
      Q9H863
      Related
      ENSP00000325717.5, ENST00000347925.9
      Conserved Domains (4) summary
      sd00038
      Location:64 → 115
      Kelch; KELCH repeat [structural motif]
      pfam13415
      Location:75 → 127
      Kelch_3; Galactose oxidase, central domain
      pfam13418
      Location:199 → 255
      Kelch_4; Galactose oxidase, central domain
      pfam13964
      Location:119 → 168
      Kelch_6; Kelch motif

    3. NM_001351937.2 → NP_001338866.1  kelch domain-containing protein 4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC010536, BC022969, KF456219
      Conserved Domains (2) summary
      sd00038
      Location:1 → 43
      Kelch; KELCH repeat [structural motif]
      cl26061
      Location:1 → 132
      PLN02193; nitrile-specifier protein

    4. NM_001351938.2 → NP_001338867.1  kelch domain-containing protein 4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC010536, BC022969, KF456219
      Conserved Domains (2) summary
      sd00038
      Location:1 → 43
      Kelch; KELCH repeat [structural motif]
      cl26061
      Location:1 → 132
      PLN02193; nitrile-specifier protein

    5. NM_017566.4 → NP_060036.2  kelch domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_060036.2

      Status: VALIDATED

      Description
      Transcript Variant: Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC022969, BP215584
      Consensus CDS
      CCDS10963.1
      UniProtKB/Swiss-Prot
      D3DUN3, D3DUN4, D3DUN5, Q8TBB5, Q96F29, Q9BVN3
      UniProtKB/TrEMBL
      Q9H863
      Related
      ENSP00000270583.4, ENST00000270583.10
      Conserved Domains (2) summary
      sd00038
      Location:64 → 115
      Kelch; KELCH repeat [structural motif]
      cl26061
      Location:77 → 313
      PLN02193; nitrile-specifier protein

    RNA

    1. NR_147833.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC010536, BC022969, KF456219
      Related
      ENST00000562155.5

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      87698146..87765986 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434252.1 → XP_047290208.1  kelch domain-containing protein 4 isoform X1

    2. XM_047434253.1 → XP_047290209.1  kelch domain-containing protein 4 isoform X1

    3. XM_047434255.1 → XP_047290211.1  kelch domain-containing protein 4 isoform X1

    4. XM_047434254.1 → XP_047290210.1  kelch domain-containing protein 4 isoform X1

    5. XM_024450318.1 → XP_024306086.1  kelch domain-containing protein 4 isoform X1

      Related
      ENST00000566349.5
      Conserved Domains (2) summary
      sd00038
      Location:1 → 43
      Kelch; KELCH repeat [structural motif]
      cl26061
      Location:1 → 132
      PLN02193; nitrile-specifier protein

    6. XM_047434257.1 → XP_047290213.1  kelch domain-containing protein 4 isoform X2

    7. XM_047434256.1 → XP_047290212.1  kelch domain-containing protein 4 isoform X2

    RNA

    1. XR_001751943.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      93769791..93838649 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380529.1 → XP_054236504.1  kelch domain-containing protein 4 isoform X1

    2. XM_054380528.1 → XP_054236503.1  kelch domain-containing protein 4 isoform X1

    3. XM_054380531.1 → XP_054236506.1  kelch domain-containing protein 4 isoform X1

    4. XM_054380527.1 → XP_054236502.1  kelch domain-containing protein 4 isoform X1

    5. XM_054380535.1 → XP_054236510.1  kelch domain-containing protein 4 isoform X1

    6. XM_054380530.1 → XP_054236505.1  kelch domain-containing protein 4 isoform X1

    7. XM_054380532.1 → XP_054236507.1  kelch domain-containing protein 4 isoform X1

    8. XM_054380534.1 → XP_054236509.1  kelch domain-containing protein 4 isoform X2

    9. XM_054380533.1 → XP_054236508.1  kelch domain-containing protein 4 isoform X2

    RNA

    1. XR_008489100.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_024488.1: Suppressed sequence

      Description
      NR_024488.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TBB5.1 GenPept UniProtKB/Swiss-Prot:Q8TBB5

    Gene LinkOut

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

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