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KLHL29 kelch like family member 29 [ Homo sapiens (human) ]

Gene ID: 114818, updated on 5-Mar-2024

Summary

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Official Symbol
KLHL29provided by HGNC
Official Full Name
kelch like family member 29provided by HGNC
Primary source
HGNC:HGNC:29404
See related
Ensembl:ENSG00000119771 AllianceGenome:HGNC:29404
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
KBTBD9
Expression
Ubiquitous expression in adrenal (RPKM 5.0), prostate (RPKM 2.9) and 24 other tissues See more
Orthologs
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Genomic context

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See KLHL29 in Genome Data Viewer
Location:
2p24.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (23385179..23708606)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (23420561..23743675)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (23608050..23931476)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985792 Neighboring gene uncharacterized LOC107985858 Neighboring gene uncharacterized LOC102723389 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:23453551-23454248 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:23520344-23520844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:23570305-23570998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15411 Neighboring gene Sharpr-MPRA regulatory region 13479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11220 Neighboring gene long intergenic non-protein coding RNA 2923 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23620049-23620548 Neighboring gene NANOG hESC enhancer GRCh37_chr2:23627224-23627805 Neighboring gene Sharpr-MPRA regulatory region 1613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23642945-23643779 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:23648459-23648959 Neighboring gene uncharacterized LOC124907741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23675903-23676404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23676405-23676904 Neighboring gene peptidylprolyl isomerase A pseudogene 61 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23709146-23709646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23710559-23711060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23711061-23711560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:23720142-23720825 Neighboring gene uncharacterized LOC105374325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23727033-23727581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23728885-23729385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23739883-23740383 Neighboring gene NANOG hESC enhancer GRCh37_chr2:23742998-23743499 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:23746074-23747273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23758787-23759662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23768135-23768636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:23776477-23777416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:23777417-23778356 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:23786903-23787264 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:23805267-23805410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23824976-23825531 Neighboring gene uncharacterized LOC102723401 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23891284-23891901 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23891902-23892518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23894797-23895296 Neighboring gene MPRA-validated peak3617 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:23911725-23912270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:23925627-23926459 Neighboring gene ATPase family AAA domain containing 2B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15416 Neighboring gene MPRA-validated peak3620 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15417 Neighboring gene phosphoglycerate mutase 1 pseudogene 6 Neighboring gene ribosomal protein S13 pseudogene 4

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. The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus. Sun Z, et al. Cancer, 2017 May 1. PMID 28081303, Free PMC Article
  2. Genome-Wide Analysis in Brazilians Reveals Highly Differentiated Native American Genome Regions. Mychaleckyj JC, et al. Mol Biol Evol, 2017 Mar 1. PMID 28100790, Free PMC Article
  3. Cullin-3-KCTD10-mediated CEP97 degradation promotes primary cilium formation. Nagai T, et al. J Cell Sci, 2018 Dec 12. PMID 30404837
  4. Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. Murea M, et al. Am J Nephrol, 2011. PMID 21546767, Free PMC Article
  5. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. Lettre G, et al. PLoS Genet, 2011 Feb 10. PMID 21347282, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. KLHL29-mediated DDX3X degradation promotes chemosensitivity by abrogating cell cycle checkpoint in triple-negative breast cancer.
    Title: KLHL29-mediated DDX3X degradation promotes chemosensitivity by abrogating cell cycle checkpoint in triple-negative breast cancer.
  2. The fusion transcript NR5A2-KLHL29FT was identified in normal and cancerous colonic epithelia. It is due to an uncharacterized polymorphic germline insertion of the NR5A2 sequence from chromosome 1 into the KLHL29 locus at chromosome 2, rather than a chromosomal rearrangement. NR5A2-KLH29FT expression levels were significantly lower in colon cancers than in matched normal colonic epithelia.
    Title: The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus.
  3. Brazilian Amerindian ancestry compared to Asian, European, and African Genomes.SNPs within or proximal to CIITA (rs6498115), SMC6 (rs1834619), and KLHL29 (rs2288697) were most differentiated in the Amerindian-specific branch. SNPs in ADAMTS9 (rs7631391), DOCK2 (rs77594147), SLC28A1 (rs28649017), ARHGAP5 (rs7151991), and CIITA (rs45601437) in the Asian comparison.
    Title: Genome-Wide Analysis in Brazilians Reveals Highly Differentiated Native American Genome Regions.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  5. 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.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
EBI GWAS Catalog
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
EBI GWAS Catalog
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

  • KIAA1921

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-like protein 29
Names
kelch repeat and BTB (POZ) domain containing 9
kelch repeat and BTB domain-containing protein 9
kelch-like 29

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_052920.2 → NP_443152.1  kelch-like protein 29

    See identical proteins and their annotated locations for NP_443152.1

    Status: VALIDATED

    Source sequence(s)
    AB067508, AC011239, AC012506, BC013982, BE142100, DR002067
    Consensus CDS
    CCDS54335.1
    UniProtKB/Swiss-Prot
    Q8N388, Q96BF0, Q96CT2, Q96PW7
    Related
    ENSP00000420659.1, ENST00000486442.6
    Conserved Domains (6) summary
    smart00612
    Location:822 → 870
    Kelch; Kelch domain
    PHA03098
    Location:333 → 860
    PHA03098; kelch-like protein; Provisional
    sd00038
    Location:673 → 716
    Kelch; KELCH repeat [structural motif]
    pfam00651
    Location:319 → 427
    BTB; BTB/POZ domain
    pfam01344
    Location:672 → 717
    Kelch_1; Kelch motif
    pfam07707
    Location:436 → 537
    BACK; BTB And C-terminal Kelch

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    23385179..23708606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006711929.4 → XP_006711992.1  kelch-like protein 29 isoform X1

    See identical proteins and their annotated locations for XP_006711992.1

    UniProtKB/Swiss-Prot
    Q8N388, Q96BF0, Q96CT2, Q96PW7
    Conserved Domains (6) summary
    smart00612
    Location:822 → 870
    Kelch; Kelch domain
    PHA03098
    Location:333 → 860
    PHA03098; kelch-like protein; Provisional
    sd00038
    Location:673 → 716
    Kelch; KELCH repeat [structural motif]
    pfam00651
    Location:319 → 427
    BTB; BTB/POZ domain
    pfam01344
    Location:672 → 717
    Kelch_1; Kelch motif
    pfam07707
    Location:436 → 537
    BACK; BTB And C-terminal Kelch

  2. XM_011532501.3 → XP_011530803.1  kelch-like protein 29 isoform X2

    Conserved Domains (6) summary
    smart00612
    Location:516 → 564
    Kelch; Kelch domain
    PHA03098
    Location:27 → 554
    PHA03098; kelch-like protein; Provisional
    sd00038
    Location:367 → 410
    Kelch; KELCH repeat [structural motif]
    pfam00651
    Location:13 → 121
    BTB; BTB/POZ domain
    pfam01344
    Location:366 → 411
    Kelch_1; Kelch motif
    pfam07707
    Location:130 → 231
    BACK; BTB And C-terminal Kelch

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    23420561..23743675
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054340358.1 → XP_054196333.1  kelch-like protein 29 isoform X1

    UniProtKB/Swiss-Prot
    Q8N388, Q96BF0, Q96CT2, Q96PW7

  2. XM_054340357.1 → XP_054196332.1  kelch-like protein 29 isoform X1

    UniProtKB/Swiss-Prot
    Q8N388, Q96BF0, Q96CT2, Q96PW7

  3. XM_054340359.1 → XP_054196334.1  kelch-like protein 29 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_025067.1: Suppressed sequence

    Description
    NM_025067.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96CT2.3 GenPept UniProtKB/Swiss-Prot:Q96CT2

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