KLHL5

gene
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Summary

KLHL5 (kelch like family member 5, HGNC:6356) is a protein-coding gene on chromosome 4p14, encoding Kelch-like protein 5 (Q96PQ7).

Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Located in microtubule cytoskeleton and plasma membrane. Implicated in cocaine dependence.

Source: NCBI Gene 51088 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 112 total
  • MANE Select transcript: NM_015990

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6356
Approved symbolKLHL5
Namekelch like family member 5
Location4p14
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000109790
Ensembl biotypeprotein_coding
OMIM608064
Entrez51088

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 nonsense_mediated_decay

ENST00000261425, ENST00000261426, ENST00000381930, ENST00000504108, ENST00000508137, ENST00000514399, ENST00000515612, ENST00000891918, ENST00000891919, ENST00000891920, ENST00000891921, ENST00000919279, ENST00000962795

RefSeq mRNA: 4 — MANE Select: NM_015990 NM_001007075, NM_001171654, NM_015990, NM_199039

CCDS: CCDS33975, CCDS3449, CCDS54756

Canonical transcript exons

ENST00000504108 — 11 exons

ExonStartEnd
ENSE000007106633911302039113232
ENSE000008264433910756939107731
ENSE000010771913911515939115330
ENSE000011714923908110339081239
ENSE000013012063909669239096878
ENSE000013049523908196339082159
ENSE000013053943910328739103511
ENSE000013267013908651539086727
ENSE000020492013906223239063035
ENSE000020713173912101039126233
ENSE000034772653907596539076147

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 96.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.2748 / max 426.3441, expressed in 1803 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
4735716.65401772
4735814.62341754
473565.14831610
473590.2644116
473600.217681
2031420.134252
473610.130651
473620.102352

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225596.52gold quality
seminal vesicleUBERON:000099896.32gold quality
corpus callosumUBERON:000233695.11gold quality
cauda epididymisUBERON:000436094.84gold quality
C1 segment of cervical spinal cordUBERON:000646994.81gold quality
spinal cordUBERON:000224094.78gold quality
smooth muscle tissueUBERON:000113594.57gold quality
subthalamic nucleusUBERON:000190694.20gold quality
substantia nigraUBERON:000203893.85gold quality
amygdalaUBERON:000187693.76gold quality
Ammon’s hornUBERON:000195493.67gold quality
placentaUBERON:000198793.65gold quality
colonic epitheliumUBERON:000039793.49gold quality
midbrainUBERON:000189193.43gold quality
Brodmann (1909) area 46UBERON:000648393.34gold quality
muscle layer of sigmoid colonUBERON:003580593.26gold quality
postcentral gyrusUBERON:000258193.17gold quality
inferior vagus X ganglionUBERON:000536392.84gold quality
hypothalamusUBERON:000189892.82gold quality
islet of LangerhansUBERON:000000692.78gold quality
medulla oblongataUBERON:000189692.76gold quality
dorsal plus ventral thalamusUBERON:000189792.70gold quality
lower esophagus muscularis layerUBERON:003583392.45gold quality
lower esophagusUBERON:001347392.43gold quality
cortical plateUBERON:000534392.36gold quality
vermiform appendixUBERON:000115492.30gold quality
monocyteCL:000057692.24gold quality
superficial temporal arteryUBERON:000161492.21gold quality
parietal lobeUBERON:000187292.13gold quality
temporal lobeUBERON:000187192.05gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-137537yes7.58
E-ANND-3yes5.57
E-GEOD-99795no76.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

203 targeting KLHL5, 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-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4262100.0073.263931
HSA-MIR-3646100.0073.565283
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3163100.0077.238605
HSA-MIR-656-3P100.0072.152788
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-477599.9875.006394
HSA-MIR-569699.9872.364487
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-433-3P99.9869.371203
HSA-MIR-480399.9871.993117
HSA-MIR-1213699.9872.815713
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-60799.9773.625593
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-50799.9770.111915
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-590-3P99.9674.346478
HSA-MIR-1250-3P99.9670.044038

Literature-anchored findings (GeneRIF, showing 2)

  • Data report a novel splicing variant of KLHL5, named KLHL5b, and describe its expression pattern in many tissues. (PMID:14672410)
  • KLHL5/Cul3-based E3 ubiquitin ligase complex is important for regulation of SK1 protein stability via Lys183 ubiquitination. (PMID:31652307)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioklhl5ENSDARG00000062122
mus_musculusKlhl5ENSMUSG00000054920
rattus_norvegicusKlhl5ENSRNOG00000008421
drosophila_melanogasterCG17754FBGN0030114

Paralogs (54): KLHL13 (ENSG00000003096), KLHL20 (ENSG00000076321), KEAP1 (ENSG00000079999), KLHL42 (ENSG00000087448), KLHL22 (ENSG00000099910), KLHL4 (ENSG00000102271), KLHL2 (ENSG00000109466), BACH2 (ENSG00000112182), KLHL18 (ENSG00000114648), KLHL24 (ENSG00000114796), IVNS1ABP (ENSG00000116679), KLHL12 (ENSG00000117153), KLHL29 (ENSG00000119771), 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 5Q96PQ7 (reviewed: Q96PQ7)

All UniProt accessions (5): Q96PQ7, A0A804C9D6, A0A804CHP1, H0Y9Y5, H0YAF6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Expressed in adrenal gland, ovary and thyroid gland and less abundantly in lymph node, prostate, spinal cord, testis and trachea.

Miscellaneous. May be due to intron retention. Ubiquitous expression, differentially expressed in kidney and pancreas relatively to isoform 1.

Isoforms (6)

UniProt IDNamesCanonical?
Q96PQ7-11, KLHL5ayes
Q96PQ7-22
Q96PQ7-33
Q96PQ7-44, KLHL5b
Q96PQ7-55
Q96PQ7-66

RefSeq proteins (4): NP_001007076, NP_001165125, NP_057074, NP_950240 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR006652Kelch_1Repeat
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR011705BACKDomain
IPR015915Kelch-typ_b-propellerHomologous_superfamily
IPR030606KLHL5_BTB/POZDomain
IPR056737Beta-prop_ATRN-MKLN-likeDomain

Pfam: PF00651, PF07707, PF24981

UniProt features (26 total): sequence conflict 8, repeat 6, splice variant 5, compositionally biased region 2, sequence variant 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96PQ7-F177.740.66

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-8951664Neddylation
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1280218Adaptive Immune System
R-HSA-168256Immune System
R-HSA-392499Metabolism of proteins
R-HSA-597592Post-translational protein modification
R-HSA-983169Class I MHC mediated antigen processing & presentation

MSigDB gene sets: 162 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, LHX3_01, NKX61_01, WTGAAAT_UNKNOWN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GATA2_01, BENPORATH_NOS_TARGETS, GOMF_ACTIN_BINDING

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

GO Molecular Function (3): actin binding (GO:0003779), ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515)

GO Cellular Component (6): cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), microtubule cytoskeleton (GO:0015630), Cul3-RING ubiquitin ligase complex (GO:0031463), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Post-translational protein modification1
Class I MHC mediated antigen processing & presentation1
Immune System1
Metabolism of proteins1
Adaptive Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
cytoskeletal protein binding1
enzyme-substrate adaptor activity1
binding1
intracellular anatomical structure1
cytoplasm1
membrane1
cell periphery1
cytoskeleton1
cullin-RING ubiquitin ligase complex1
intracellular membraneless organelle1

Protein interactions and networks

STRING

764 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KLHL5TMEM156Q8N614636
KLHL5PRKAR2BP31323571
KLHL5ANAPC7Q9UJX3539
KLHL5N4BP2Q86UW6489
KLHL5WDR19Q8NEZ3489
KLHL5NEDD4LQ96PU5481
KLHL5LIASO43766476
KLHL5SIAH2O43255467
KLHL5RFC1P35251449
KLHL5ZNF684Q5T5D7442
KLHL5FBXO48Q5FWF7439
KLHL5OR8B4Q96RC9429
KLHL5SOCS3O14543424
KLHL5OR5AP2Q8NGF4417
KLHL5RPL9P32969414

IntAct

29 interactions, top by confidence:

ABTypeScore
CUL3KLHL5psi-mi:“MI:0915”(physical association)0.800
KLHL5CUL3psi-mi:“MI:0914”(association)0.800
TRIM2TRIM3psi-mi:“MI:0914”(association)0.770
KLHL1CUL3psi-mi:“MI:0914”(association)0.560
CUL3RHOBTB1psi-mi:“MI:0914”(association)0.530
CUL3ZSWIM8psi-mi:“MI:0914”(association)0.530
SKA2VSIG8psi-mi:“MI:0914”(association)0.530
SPHK1KLHL5psi-mi:“MI:0915”(physical association)0.480
GABARAPL2KLHL5psi-mi:“MI:0915”(physical association)0.370
KLHL5MAP1LC3Bpsi-mi:“MI:0915”(physical association)0.370
SMN1KLHL5psi-mi:“MI:0915”(physical association)0.370
TK1KLHL5psi-mi:“MI:0915”(physical association)0.370
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
KLHL4CUL1psi-mi:“MI:0914”(association)0.350
SKA2CORO1Apsi-mi:“MI:0914”(association)0.350
KLHL1SNX2psi-mi:“MI:0914”(association)0.350
CAMK2DPPM1Dpsi-mi:“MI:0914”(association)0.350
MYCKLHL5psi-mi:“MI:0915”(physical association)0.000
KLHL5psi-mi:“MI:0915”(physical association)0.000
KLHL5psi-mi:“MI:0915”(physical association)0.000
KLHL5hscCpsi-mi:“MI:0915”(physical association)0.000
fliHKLHL5psi-mi:“MI:0915”(physical association)0.000

BioGRID (28): KLHL5 (Affinity Capture-MS), KLHL5 (Two-hybrid), SPHK1 (Affinity Capture-Western), CUL3 (Affinity Capture-Western), KLHL5 (Affinity Capture-MS), KLHL5 (Affinity Capture-MS), KLHL5 (Affinity Capture-MS), KLHL5 (Affinity Capture-MS), KLHL5 (Affinity Capture-MS), KLHL5 (Reconstituted Complex), KLHL5 (Affinity Capture-MS), KLHL5 (Negative Genetic), KLHL5 (Negative Genetic), KLHL5 (Affinity Capture-MS), CUL3 (Affinity Capture-Western)

ESM2 similar proteins: A4FUN7, A5D9H7, A5PKA5, A5WWB0, A6H8I0, A6NNY8, C0HB46, D0RB01, F1M625, O75317, O89050, P0C8Z3, P50876, P50904, P62068, P62069, Q09LZ8, Q3TIX9, Q3UHD6, Q52KZ6, Q53GS9, Q5DU02, Q5F415, Q5F450, Q5IFJ9, Q5IS37, Q5IS82, Q5M981, Q5R4Q7, Q5R573, Q5R761, Q5RB35, Q5RBQ4, Q5RDP3, Q5VU57, Q60969, Q6DCJ1, Q6GNI6, Q8CEG8, Q8K4V4

Diamond homologs: A0A1B8YAB1, A1YPR0, B0WWP2, B1H285, B3M9V8, B3NDN0, B4GRJ2, B4HIK1, B4J045, B4L0G9, B4LIG6, B4MXW3, B4PD06, B4QLQ2, C9JR72, D3Z8N4, E0CZ16, G3X9X1, O15062, O88939, O93567, O95365, P28575, P41182, P41183, Q08CL3, Q08DK3, Q13105, Q16RL8, Q2M0J9, Q3UQV5, Q52KB5, Q5EXX3, Q5R7B8, Q5RDY3, Q5TC79, Q5ZI33, Q5ZKD9, Q5ZM39, Q60821

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 23 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
proteasome-mediated ubiquitin-dependent protein catabolic process718.3×1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance91
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1961 predictions. Top by Δscore:

VariantEffectΔscore
4:39045094:GCG:Gdonor_gain1.0000
4:39045095:CGGTA:Cdonor_loss1.0000
4:39045097:G:GGdonor_gain1.0000
4:39045097:GT:Gdonor_loss1.0000
4:39045098:T:Gdonor_loss1.0000
4:39075959:TTTCA:Tacceptor_loss1.0000
4:39075961:TCAG:Tacceptor_loss1.0000
4:39075962:CA:Cacceptor_loss1.0000
4:39081099:ACAG:Aacceptor_loss1.0000
4:39081100:CA:Cacceptor_loss1.0000
4:39081101:A:ACacceptor_loss1.0000
4:39081101:A:AGacceptor_gain1.0000
4:39081101:AGATT:Aacceptor_gain1.0000
4:39081102:G:GGacceptor_gain1.0000
4:39081102:G:GTacceptor_loss1.0000
4:39081102:GATTG:Gacceptor_gain1.0000
4:39081236:ACAG:Adonor_loss1.0000
4:39081238:AG:Adonor_loss1.0000
4:39081239:GGTAA:Gdonor_loss1.0000
4:39081241:T:Gdonor_loss1.0000
4:39081961:A:Gacceptor_gain1.0000
4:39086674:A:Tdonor_gain1.0000
4:39086677:GATC:Gdonor_gain1.0000
4:39086680:C:CGdonor_gain1.0000
4:39086680:C:Gdonor_gain1.0000
4:39086684:G:GGdonor_gain1.0000
4:39088169:T:TGdonor_gain1.0000
4:39096690:A:AGacceptor_gain1.0000
4:39096691:G:GGacceptor_gain1.0000
4:39096826:G:GTdonor_gain1.0000

AlphaMissense

4959 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:39076104:G:CD221H1.000
4:39076105:A:CD221A1.000
4:39076105:A:GD221G1.000
4:39076105:A:TD221V1.000
4:39076114:T:CL224S1.000
4:39076141:C:AA233D1.000
4:39076143:C:GH234D1.000
4:39076144:A:GH234R1.000
4:39076147:G:CR235T1.000
4:39081103:A:CR235S1.000
4:39081103:A:TR235S1.000
4:39081105:T:GL236W1.000
4:39081108:T:AV237E1.000
4:39081111:T:AL238H1.000
4:39081111:T:CL238P1.000
4:39081111:T:GL238R1.000
4:39081128:T:CY244H1.000
4:39081131:T:CF245L1.000
4:39081132:T:CF245S1.000
4:39081133:T:AF245L1.000
4:39081133:T:GF245L1.000
4:39081141:T:CM248T1.000
4:39081142:G:AM248I1.000
4:39081142:G:CM248I1.000
4:39081142:G:TM248I1.000
4:39081143:T:AF249I1.000
4:39081143:T:CF249L1.000
4:39081143:T:GF249V1.000
4:39081144:T:CF249S1.000
4:39081144:T:GF249C1.000

dbSNP variants (sampled 300 via entrez): RS1000033272 (4:39127487 G>A), RS1000048856 (4:39052640 C>G), RS1000066156 (4:39130532 T>G), RS1000112032 (4:39079851 G>C), RS1000124415 (4:39072991 T>A), RS1000160367 (4:39130828 G>A), RS1000225942 (4:39113588 A>G), RS1000226967 (4:39094342 G>T), RS1000233297 (4:39065575 A>G), RS1000234354 (4:39073277 A>G), RS10002441 (4:39096149 T>C), RS1000251037 (4:39073272 T>A,C), RS1000320211 (4:39137038 A>G), RS1000336059 (4:39058371 A>G), RS1000339285 (4:39115526 A>G,T)

Disease associations

OMIM: gene MIM:608064 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST002088_4Asthma (childhood onset)3.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression5
sodium arsenitedecreases expression, increases expression2
Acetaminophendecreases expression2
Benzo(a)pyreneaffects methylation, increases expression2
Cisplatinaffects expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Smokedecreases expression, increases abundance2
Cyclosporinedecreases expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
mercuric bromideaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
entinostatincreases expression1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, increases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
MT19c compoundincreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomidedecreases expression1
Decitabineaffects expression1
Troglitazoneincreases expression1
Vorinostatincreases expression1
Leflunomideincreases expression1
Air Pollutantsdecreases expression, increases abundance1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.