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

Gene ID: 54758, updated on 5-Mar-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
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Genomic context

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Location:
16q24.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (87698146..87765986, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (93769791..93838649, complement)
105.20220307 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. Huntington Disease-Like 2. Adam MP, et al. , 1993. PMID 20301701
  3. 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
  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 (30) 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)

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

  • 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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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_2023_10

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

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