KLHL29

gene
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Also known as KIAA1921

Summary

KLHL29 (kelch like family member 29, HGNC:29404) is a protein-coding gene on chromosome 2p24.1, encoding Kelch-like protein 29 (Q96CT2).

Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul3-RING ubiquitin ligase complex. Predicted to be active in cytoplasm.

Source: NCBI Gene 114818 — RefSeq curated summary.

At a glance

  • GWAS associations: 37
  • Clinical variants (ClinVar): 73 total
  • MANE Select transcript: NM_052920

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29404
Approved symbolKLHL29
Namekelch like family member 29
Location2p24.1
Locus typegene with protein product
StatusApproved
AliasesKIAA1921
Ensembl geneENSG00000119771
Ensembl biotypeprotein_coding
Entrez114818

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 retained_intron

ENST00000288548, ENST00000471654, ENST00000486442, ENST00000489446, ENST00000869654, ENST00000970997, ENST00000970998, ENST00000970999

RefSeq mRNA: 1 — MANE Select: NM_052920 NM_052920

CCDS: CCDS54335

Canonical transcript exons

ENST00000486442 — 14 exons

ExonStartEnd
ENSE000010345782368439923684537
ENSE000010707032369167423691876
ENSE000018214182364233823642850
ENSE000018389412347556023475667
ENSE000018772822370648123708606
ENSE000018878602338517923385780
ENSE000034825432369595123696133
ENSE000035178322356215223562481
ENSE000035452202369562323695821
ENSE000035469642370371923703863
ENSE000036046772363913923639280
ENSE000036067812369633323696513
ENSE000036180642369326923693528
ENSE000036941192370318623703379

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 91.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.1269 / max 51.3915, expressed in 1284 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
191532.19681105
191541.9301836

Top tissues by expression

290 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097991.98gold quality
middle temporal gyrusUBERON:000277190.71gold quality
sural nerveUBERON:001548890.56gold quality
Brodmann (1909) area 23UBERON:001355490.37gold quality
synovial jointUBERON:000221787.68gold quality
pigmented layer of retinaUBERON:000178287.51gold quality
trigeminal ganglionUBERON:000167586.09gold quality
lateral nuclear group of thalamusUBERON:000273685.11gold quality
skin of hipUBERON:000155484.03gold quality
cortical plateUBERON:000534383.97gold quality
endothelial cellCL:000011583.61silver quality
nerveUBERON:000102183.60gold quality
tibial nerveUBERON:000132383.60gold quality
lower esophagus muscularis layerUBERON:003583383.06gold quality
lower esophagusUBERON:001347382.98gold quality
calcaneal tendonUBERON:000370182.73gold quality
dorsal root ganglionUBERON:000004482.48gold quality
parietal pleuraUBERON:000240082.24gold quality
adrenal cortexUBERON:000123582.21gold quality
left adrenal gland cortexUBERON:003582581.58gold quality
superior frontal gyrusUBERON:000266181.49gold quality
upper leg skinUBERON:000426281.29gold quality
urethraUBERON:000005781.23gold quality
saphenous veinUBERON:000731881.18gold quality
gastrocnemiusUBERON:000138881.05gold quality
right adrenal gland cortexUBERON:003582781.00gold quality
left adrenal glandUBERON:000123480.97gold quality
primary visual cortexUBERON:000243680.83gold quality
esophagogastric junction muscularis propriaUBERON:003584180.80gold quality
postcentral gyrusUBERON:000258180.75gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-CURD-119yes31.22
E-ANND-3no4.53

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

miRNA regulators (miRDB)

225 targeting KLHL29, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692A100.0074.406850
HSA-MIR-4262100.0073.263931
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-188-3P100.0068.761240
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-4673100.0066.641490
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-3646100.0073.565283
HSA-MIR-3163100.0077.238605
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997

Literature-anchored findings (GeneRIF, showing 3)

  • 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. (PMID:28081303)
  • 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. (PMID:28100790)
  • KLHL29-mediated DDX3X degradation promotes chemosensitivity by abrogating cell cycle checkpoint in triple-negative breast cancer. (PMID:37845393)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioKLHL29ENSDARG00000043799
danio_rerioklhl29ENSDARG00000087688
mus_musculusKlhl29ENSMUSG00000020627
rattus_norvegicusKlhl29ENSRNOG00000005371

Paralogs (54): KLHL13 (ENSG00000003096), KLHL20 (ENSG00000076321), KEAP1 (ENSG00000079999), KLHL42 (ENSG00000087448), KLHL22 (ENSG00000099910), KLHL4 (ENSG00000102271), KLHL2 (ENSG00000109466), KLHL5 (ENSG00000109790), BACH2 (ENSG00000112182), KLHL18 (ENSG00000114648), KLHL24 (ENSG00000114796), IVNS1ABP (ENSG00000116679), KLHL12 (ENSG00000117153), KBTBD7 (ENSG00000120696), KLHL7 (ENSG00000122550), KLHL31 (ENSG00000124743), KLHDC7B (ENSG00000130487), KLHL36 (ENSG00000135686), KLHL8 (ENSG00000145332), KLHL3 (ENSG00000146021), KLHL35 (ENSG00000149243), KLHL1 (ENSG00000150361), BACH1 (ENSG00000156273), KLHL40 (ENSG00000157119), KLHL10 (ENSG00000161594), KLHL21 (ENSG00000162413), KLHDC8A (ENSG00000162873), KBTBD8 (ENSG00000163376), KBTBD6 (ENSG00000165572), KLHL26 (ENSG00000167487), KLHL30 (ENSG00000168427), KBTBD2 (ENSG00000170852), KLHL6 (ENSG00000172578), KLHL15 (ENSG00000174010), KLHL38 (ENSG00000175946), KBTBD11 (ENSG00000176595), KLHDC7A (ENSG00000179023), KLHL28 (ENSG00000179454), KBTBD3 (ENSG00000182359), KLHL33 (ENSG00000185271)

Protein

Protein identifiers

Kelch-like protein 29Q96CT2 (reviewed: Q96CT2)

Alternative names: Kelch repeat and BTB domain-containing protein 9

All UniProt accessions (2): Q96CT2, H0Y2P5

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt IDNamesCanonical?
Q96CT2-11yes
Q96CT2-22

RefSeq proteins (1): NP_443152* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR006652Kelch_1Repeat
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR011705BACKDomain
IPR015915Kelch-typ_b-propellerHomologous_superfamily
IPR056737Beta-prop_ATRN-MKLN-likeDomain

Pfam: PF00651, PF01344, PF07707, PF24981

UniProt features (14 total): repeat 6, compositionally biased region 2, region of interest 2, chain 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96CT2-F171.270.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, PEREZ_TP63_TARGETS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, DAWSON_METHYLATED_IN_LYMPHOMA_TCL1, LIAO_METASTASIS, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_PROTEIN_CATABOLIC_PROCESS, GOCC_TRANSFERASE_COMPLEX, GOBP_PROTEOLYSIS, GOCC_CULLIN_RING_UBIQUITIN_LIGASE_COMPLEX, GOCC_CUL3_RING_UBIQUITIN_LIGASE_COMPLEX

GO Biological Process (1): proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (2): ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515)

GO Cellular Component (2): cytoplasm (GO:0005737), Cul3-RING ubiquitin ligase complex (GO:0031463)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
enzyme-substrate adaptor activity1
binding1
intracellular anatomical structure1
cellular anatomical structure1
cullin-RING ubiquitin ligase complex1

Protein interactions and networks

STRING

526 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KLHL29FBXO46Q6PJ61479
KLHL29ABHD15Q6UXT9463
KLHL29A0A0G2JMU2A0A0G2JMU2435
KLHL29POTEB3A0JP26423
KLHL29CIMIP6Q8N5S3398
KLHL29FRMD4AQ9P2Q2384
KLHL29CIMAP1CQ8IXM7382
KLHL29CFAP68Q9H5F2380
KLHL29THOC7Q6I9Y2378
KLHL29OR2C3Q8N628377
KLHL29FBXW5Q969U6366
KLHL29MINDY4Q4G0A6353
KLHL29GPATCH11Q8N954349
KLHL29DENND4CQ5VZ89344
KLHL29CEACAM18A8MTB9342

IntAct

11 interactions, top by confidence:

ABTypeScore
KLHL29NUDCD3psi-mi:“MI:0915”(physical association)0.670
KLHL9ENC1psi-mi:“MI:0914”(association)0.640
KLHL29HSP90AB1psi-mi:“MI:0915”(physical association)0.400
ZNF232ZNF197psi-mi:“MI:0914”(association)0.350
KLHL29NPHP3psi-mi:“MI:0914”(association)0.350
repVWA8psi-mi:“MI:0914”(association)0.350
ZBTB7CZBTB5psi-mi:“MI:0914”(association)0.350
KLHL29TRIM32psi-mi:“MI:0914”(association)0.350

BioGRID (46): KBTBD8 (Affinity Capture-MS), ZBTB10 (Affinity Capture-MS), NPHP3 (Affinity Capture-MS), KLHL29 (Affinity Capture-MS), KLHL21 (Affinity Capture-MS), NUDCD3 (Affinity Capture-MS), KBTBD7 (Affinity Capture-MS), KLHL29 (Affinity Capture-RNA), KLHL29 (Affinity Capture-RNA), KLHL29 (Affinity Capture-Western), ZBTB10 (Affinity Capture-MS), KLHL29 (Affinity Capture-MS), NUDCD3 (Affinity Capture-MS), NPHP3 (Affinity Capture-MS), KBTBD7 (Affinity Capture-MS)

ESM2 similar proteins: D3ZB51, E9PZ19, M0RAS4, O60242, O60245, O70472, O75882, O94779, P13590, P13591, P13595, P13596, P15209, P24786, P31836, P51641, P68500, P78539, P97300, P97527, P97546, Q01973, Q03351, Q15223, Q16288, Q16620, Q5IFJ9, Q5IS37, Q5IS82, Q63604, Q63769, Q6A051, Q6AZB0, Q6P1D5, Q6VNS1, Q7TNR6, Q80T74, Q80ZF8, Q8R4I7, Q8TDF5

Diamond homologs: A0JN76, A1L2U9, A1YPR0, B1WAZ8, B1WBS3, B1WBU4, B2RXF5, E1B932, G5E8B9, O14867, O15062, O43167, O43298, O88282, O88939, O93567, O95365, O95625, P10074, P28575, P41182, P41183, P52739, P97302, P97303, Q0IH98, Q0IJ29, Q0P4X6, Q0VCJ6, Q13105, Q14526, Q1H9T6, Q1L8W0, Q3B725, Q3B7M1, Q3B7N9, Q3SWU4, Q3ZB90, Q503R4, Q53G59

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

73 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance70
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4573 predictions. Top by Δscore:

VariantEffectΔscore
2:23445146:GGCAT:Gdonor_gain1.0000
2:23475558:A:AGacceptor_gain1.0000
2:23475559:G:GGacceptor_gain1.0000
2:23475664:CAAG:Cdonor_loss1.0000
2:23475665:AAGG:Adonor_loss1.0000
2:23475667:GGT:Gdonor_loss1.0000
2:23475668:G:GAdonor_loss1.0000
2:23475669:T:Adonor_loss1.0000
2:23562147:CACA:Cacceptor_loss1.0000
2:23562149:CAG:Cacceptor_loss1.0000
2:23562150:A:ATacceptor_loss1.0000
2:23562478:CAAGG:Cdonor_loss1.0000
2:23562479:AAGG:Adonor_loss1.0000
2:23562481:GGT:Gdonor_loss1.0000
2:23562482:GT:Gdonor_loss1.0000
2:23562483:T:Adonor_loss1.0000
2:23691875:CGG:Cdonor_loss1.0000
2:23691877:G:Adonor_loss1.0000
2:23691877:G:GGdonor_gain1.0000
2:23691878:T:Adonor_loss1.0000
2:23693524:CACAG:Cdonor_loss1.0000
2:23693526:CAGG:Cdonor_loss1.0000
2:23693527:AGG:Adonor_loss1.0000
2:23693528:GG:Gdonor_loss1.0000
2:23693529:GT:Gdonor_loss1.0000
2:23693530:T:Gdonor_loss1.0000
2:23695614:A:AGacceptor_gain1.0000
2:23695617:CTGCA:Cacceptor_loss1.0000
2:23695618:TGCA:Tacceptor_loss1.0000
2:23695619:GCA:Gacceptor_loss1.0000

AlphaMissense

5688 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:23642826:T:CF306L1.000
2:23642827:T:CF306S1.000
2:23642828:C:AF306L1.000
2:23642828:C:GF306L1.000
2:23684425:C:AR323S1.000
2:23684426:G:CR323P1.000
2:23684450:T:CL331P1.000
2:23684485:C:GH343D1.000
2:23684495:T:AV346D1.000
2:23684509:A:CS351R1.000
2:23684511:C:AS351R1.000
2:23684511:C:GS351R1.000
2:23691765:T:CF391L1.000
2:23691767:T:AF391L1.000
2:23691767:T:GF391L1.000
2:23691870:T:CF426L1.000
2:23691872:T:AF426L1.000
2:23691872:T:GF426L1.000
2:23693313:G:CA443P1.000
2:23693496:T:AW504R1.000
2:23693496:T:CW504R1.000
2:23695648:T:AV523D1.000
2:23695650:C:AR524S1.000
2:23695678:T:CL533P1.000
2:23695681:T:CL534P1.000
2:23695690:T:AV537D1.000
2:23695729:G:CR550P1.000
2:23695735:T:CL552P1.000
2:23695746:G:CA556P1.000
2:23695747:C:AA556D1.000

dbSNP variants (sampled 300 via entrez): RS1000005592 (2:23603894 G>A), RS1000008316 (2:23589054 C>A,G,T), RS1000011375 (2:23471710 T>G), RS1000028249 (2:23461268 G>A), RS1000028844 (2:23668973 G>A), RS1000036189 (2:23640654 C>T), RS1000040584 (2:23686261 G>A), RS1000057867 (2:23554116 G>A), RS1000059878 (2:23668680 G>A), RS1000071940 (2:23478443 T>C), RS1000072094 (2:23391852 A>G), RS1000075843 (2:23697369 G>A), RS1000082549 (2:23626829 T>G), RS1000089104 (2:23519079 G>T), RS1000089804 (2:23460115 T>C,G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

37 associations (top):

StudyTraitp-value
GCST000973_4Hypertension1.000000e-07
GCST001066_1Dialysis-related mortality8.000000e-08
GCST001762_398Obesity-related traits6.000000e-07
GCST001762_415Obesity-related traits4.000000e-06
GCST003542_1Night sleep phenotypes6.000000e-06
GCST004601_16Red blood cell count2.000000e-21
GCST004604_20Hematocrit6.000000e-09
GCST004607_212Plateletcrit7.000000e-11
GCST004608_50Granulocyte percentage of myeloid white cells2.000000e-10
GCST004615_89Hemoglobin concentration2.000000e-10
GCST004723_20Conotruncal heart defects (maternal effects)7.000000e-06
GCST006626_27Pulse pressure1.000000e-11
GCST006631_32Nicotine dependence and major depression (severity of comorbidity)8.000000e-07
GCST006922_5Regular attendance at a religious group8.000000e-09
GCST006943_64Feeling miserable3.000000e-08
GCST006945_25Feeling guilty2.000000e-09
GCST006947_34Feeling fed-up2.000000e-12
GCST007325_177General risk tolerance (MTAG)1.000000e-08
GCST007325_29General risk tolerance (MTAG)4.000000e-08
GCST007326_92Number of sexual partners7.000000e-13
GCST007709_5General factor of neuroticism1.000000e-08
GCST008034_16Hemoglobin A1c levels5.000000e-09
GCST008034_7Hemoglobin A1c levels4.000000e-11
GCST008362_99Birth weight2.000000e-16
GCST008749_1Systolic blood pressure7.000000e-07
GCST010083_273Hemoglobin levels3.000000e-12
GCST010480_2Coronary artery disease1.000000e-10
GCST011038_4Parkinson’s disease progression (motor)3.000000e-06
GCST011494_91Daytime nap4.000000e-20
GCST90000025_797Appendicular lean mass2.000000e-68

EFO canonical traits (25, from GWAS)

EFO IDTrait name
EFO:0004730hormone measurement
EFO:0003940physical activity
EFO:0004305erythrocyte count
EFO:0004348hematocrit
EFO:0007985platelet crit
EFO:0007997granulocyte percentage of myeloid white cells
EFO:0004509hemoglobin measurement
EFO:0005763pulse pressure measurement
EFO:0007006depressive symptom measurement
EFO:0009262nicotine dependence symptom count
EFO:0009592social interaction measurement
EFO:0009598feeling miserable measurement
EFO:0009595guilt measurement
EFO:0009588feeling “fed-up” measurement
EFO:0008579risk-taking behaviour
EFO:0007660neuroticism measurement
EFO:0004541HbA1c measurement
EFO:0004344birth weight
EFO:0006335systolic blood pressure
EFO:0008336disease progression measurement
EFO:0007828daytime rest measurement
EFO:0004980appendicular lean mass
EFO:0004527mean corpuscular hemoglobin
EFO:0008039BMI-adjusted hip circumference
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

51 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation9
Benzo(a)pyreneaffects methylation, decreases expression3
bisphenol Adecreases methylation, affects cotreatment, increases expression2
sodium arsenitedecreases expression2
Estradiolaffects cotreatment, increases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
aristolochic acid Idecreases expression1
trichostatin Aincreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
sulforaphanedecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
perfluorooctanoic acidincreases expression1
zinc chromatedecreases expression, increases abundance1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
chromium hexavalent iondecreases expression, increases abundance1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
ICG 001increases expression1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
bisphenol Sdecreases methylation1
jinfukangaffects cotreatment, decreases expression1
(+)-JQ1 compoundincreases expression1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects methylation1
Vehicle Emissionsdecreases methylation1
Cisplatinaffects cotreatment, decreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): conotruncal heart malformations