KLHL1

gene
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Also known as KIAA1490MRP2FLJ30047

Summary

KLHL1 (kelch like family member 1, HGNC:6352) is a protein-coding gene on chromosome 13q21.33, encoding Kelch-like protein 1 (Q9NR64). May play a role in organizing the actin cytoskeleton of the brain cells.

The KLHL1 protein belongs to a family of actin-organizing proteins related to Drosophila Kelch (Nemes et al., 2000 [PubMed 10888605]).

Source: NCBI Gene 57626 — RefSeq curated summary.

At a glance

  • GWAS associations: 18
  • Clinical variants (ClinVar): 103 total
  • MANE Select transcript: NM_020866

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6352
Approved symbolKLHL1
Namekelch like family member 1
Location13q21.33
Locus typegene with protein product
StatusApproved
AliasesKIAA1490, MRP2, FLJ30047
Ensembl geneENSG00000150361
Ensembl biotypeprotein_coding
OMIM605332
Entrez57626

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000377844, ENST00000545028

RefSeq mRNA: 2 — MANE Select: NM_020866 NM_001286725, NM_020866

CCDS: CCDS73582, CCDS9445

Canonical transcript exons

ENST00000377844 — 11 exons

ExonStartEnd
ENSE000010951326974039469740556
ENSE000010951366979673869796962
ENSE000010951386997562069975802
ENSE000010951406970762569707796
ENSE000010951426994004069940236
ENSE000010951436996130869961444
ENSE000010951466983897669839162
ENSE000010951486971936969719581
ENSE000010951506988228369882495
ENSE000014753377010720370108452
ENSE000038452736970059769701761

Expression profiles

Bgee: expression breadth broad, 60 present calls, max score 95.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.5714 / max 142.4535, expressed in 88 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1375350.332969
1375340.191733
1375360.046818

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
substantia nigra pars reticulataUBERON:000196695.98gold quality
substantia nigra pars compactaUBERON:000196594.98gold quality
cortical plateUBERON:000534394.26gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.26gold quality
substantia nigraUBERON:000203876.62gold quality
midbrainUBERON:000189175.98gold quality
superior vestibular nucleusUBERON:000722774.09gold quality
tendon of biceps brachiiUBERON:000818870.75gold quality
ventral tegmental areaUBERON:000269169.55gold quality
ponsUBERON:000098869.54gold quality
hypothalamusUBERON:000189868.83gold quality
buccal mucosa cellCL:000233668.74gold quality
islet of LangerhansUBERON:000000663.65gold quality
triceps brachiiUBERON:000150961.92gold quality
ganglionic eminenceUBERON:000402360.91gold quality
medulla oblongataUBERON:000189660.82gold quality
prefrontal cortexUBERON:000045159.98gold quality
gluteal muscleUBERON:000200059.63gold quality
right hemisphere of cerebellumUBERON:001489059.54gold quality
anterior cingulate cortexUBERON:000983558.28gold quality
cingulate cortexUBERON:000302758.27gold quality
cerebellar vermisUBERON:000472057.98gold quality
nucleus accumbensUBERON:000188257.30gold quality
cerebellumUBERON:000203756.52gold quality
biceps brachiiUBERON:000150756.31gold quality
deltoidUBERON:000147656.20gold quality
amygdalaUBERON:000187656.19gold quality
cerebellar cortexUBERON:000212956.05gold quality
ventricular zoneUBERON:000305355.90gold quality
embryoUBERON:000092255.87gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-25yes1568.02
E-ANND-3yes4.25

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PITX3

miRNA regulators (miRDB)

72 targeting KLHL1, 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-5011-5P100.0083.465820
HSA-MIR-3163100.0077.238605
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-9-5P100.0072.282361
HSA-MIR-428299.9975.366408
HSA-MIR-366299.9973.825684
HSA-MIR-806899.9873.852376
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-365899.9673.874379
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-130599.9171.433443
HSA-MIR-430299.8967.941187
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-129-5P99.8870.263273
HSA-LET-7A-2-3P99.8770.531921
HSA-MIR-369-3P99.8570.522264
HSA-LET-7G-3P99.8570.431929
HSA-MIR-808099.8267.521342
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-471999.7372.103329
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-472999.6972.184233
HSA-MIR-379-3P99.6969.601524
HSA-MIR-411-3P99.6969.631524
HSA-MIR-7156-5P99.6468.811369

Literature-anchored findings (GeneRIF, showing 6)

  • This study provides, for the first time, insights into the involvement of MRP2 in neurite outgrowth, which occurs in a GSK3beta-dependent manner. (PMID:16982692)
  • modulatory effect of KLHL1 on the P/Q-type calcium channel function, suggesting a possible novel role for KLHL1 in cellular excitability. (PMID:17289272)
  • KLHL1 was expressed in human brain and kidney, but was also in other tissues, such as prostate gland, small intestine, colon, testis (but not the ovaries), liver and pancreas. (PMID:18708037)
  • KLHL1 interacts with Cav3.2 and modulates T-type calcium currents by increasing current deactivation kinetics and current density and calcium influx. (PMID:20147652)
  • Renal transplant recipients T carriers of C24T MRP2 with macrolides treatment were associated with reduced mycophenolic acid area under curve in steady-state conditions (PMID:21427078)
  • Genetic Risk of Trigger Finger: Results of a Genomewide Association Study. (PMID:32740585)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusKlhl1ENSMUSG00000022076
rattus_norvegicusKlhl1ENSRNOG00000031100

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), KLHL29 (ENSG00000119771), KBTBD7 (ENSG00000120696), KLHL7 (ENSG00000122550), KLHL31 (ENSG00000124743), KLHDC7B (ENSG00000130487), KLHL36 (ENSG00000135686), KLHL8 (ENSG00000145332), KLHL3 (ENSG00000146021), KLHL35 (ENSG00000149243), 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 1Q9NR64 (reviewed: Q9NR64)

All UniProt accessions (2): Q9NR64, F5H1J3

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in organizing the actin cytoskeleton of the brain cells.

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Highly expressed in brain.

RefSeq proteins (2): NP_001273654, NP_065917* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR006652Kelch_1Repeat
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR011705BACKDomain
IPR015915Kelch-typ_b-propellerHomologous_superfamily

Pfam: PF00651, PF01344, PF07707

UniProt features (13 total): repeat 6, compositionally biased region 3, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NR64-F179.150.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 135 (showing top): chr13q21, GOBP_DENDRITE_DEVELOPMENT, GOBP_HINDBRAIN_DEVELOPMENT, GOBP_METENCEPHALON_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GOBP_BEHAVIOR, NKX25_02, GOBP_ADULT_BEHAVIOR, AREB6_03, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEUROGENESIS, GOBP_ADULT_LOCOMOTORY_BEHAVIOR, CAGCTG_AP4_Q5, EFC_Q6, FOXD3_01

GO Biological Process (6): adult walking behavior (GO:0007628), dendrite development (GO:0016358), cerebellar Purkinje cell layer development (GO:0021680), actin cytoskeleton organization (GO:0030036), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), locomotory behavior (GO:0007626)

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

GO Cellular Component (5): cytoplasm (GO:0005737), cytoskeleton (GO:0005856), dendrite (GO:0030425), Cul3-RING ubiquitin ligase complex (GO:0031463), neuronal cell body (GO:0043025)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
anatomical structure development2
adult locomotory behavior1
walking behavior1
neuron projection development1
cerebellar cortex development1
cytoskeleton organization1
actin filament-based process1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
behavior1
cytoskeletal protein binding1
enzyme-substrate adaptor activity1
binding1
intracellular anatomical structure1
cellular anatomical structure1
intracellular membraneless organelle1
neuron projection1
dendritic tree1
cullin-RING ubiquitin ligase complex1
somatodendritic compartment1
cell body1

Protein interactions and networks

STRING

1124 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KLHL1SOCS6O14544764
KLHL1MEA1Q16626761
KLHL1TWNKQ96RR1699
KLHL1DSC3Q14574667
KLHL1DSC2Q02487648
KLHL1CALB1P05937549
KLHL1PPP2R5DQ14738496
KLHL1TTPAP49638468
KLHL1BORAQ6PGQ7447
KLHL1CACNA1HO95180444
KLHL1SLC6A11P48066436
KLHL1TAF1P21675426
KLHL1MZT1Q08AG7404
KLHL1OR5K3A6NET4400
KLHL1ATXN3P54252392

IntAct

21 interactions, top by confidence:

ABTypeScore
KLHL5CUL3psi-mi:“MI:0914”(association)0.800
KLHL1VHLpsi-mi:“MI:0915”(physical association)0.560
KLHL1CUL3psi-mi:“MI:0914”(association)0.560
CUL3KLHL1psi-mi:“MI:0915”(physical association)0.560
KLHL1NUDCD3psi-mi:“MI:0915”(physical association)0.560
HSP90AB1KLHL1psi-mi:“MI:0915”(physical association)0.400
FKBP5KLHL1psi-mi:“MI:0915”(physical association)0.400
KLHL1psi-mi:“MI:0915”(physical association)0.400
KLHL1HSP90AA1psi-mi:“MI:0915”(physical association)0.400
CACYBPKLHL1psi-mi:“MI:0915”(physical association)0.400
NUDCD2KLHL1psi-mi:“MI:0915”(physical association)0.400
NEK4QSOX1psi-mi:“MI:0914”(association)0.350
KLHL4CUL1psi-mi:“MI:0914”(association)0.350
CUL3ZBTB24psi-mi:“MI:0914”(association)0.350
KLHL1SNX2psi-mi:“MI:0914”(association)0.350

BioGRID (25): KLHL1 (PCA), KLHL1 (Affinity Capture-MS), KLHL1 (Affinity Capture-Western), ARHGEF7 (Affinity Capture-MS), RNASEH2A (Affinity Capture-MS), NUDCD3 (Affinity Capture-MS), GIT1 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX1 (Affinity Capture-MS), SNX6 (Affinity Capture-MS), KLHL5 (Affinity Capture-MS), MISP (Affinity Capture-MS), KLHL1 (Affinity Capture-MS), KLHL1 (Negative Genetic), CUL3 (Affinity Capture-Western)

ESM2 similar proteins: A1A5C7, A5D7B1, A6H7A0, A6NCF5, A6QLN9, A8MUP2, D3YYU8, D3ZZ80, O43688, O75147, O88843, P08887, Q14CX5, Q3SZQ2, Q3UHH2, Q58CT4, Q5EA19, Q5R4Q7, Q5R7S9, Q5RCI5, Q5RFN0, Q5SP67, Q5SUV1, Q642A6, Q6IA17, Q6PCB0, Q7TPB4, Q86TI4, Q8BGR6, Q8BZI6, Q8K5A4, Q8N5I2, Q8N653, Q8R2Z5, Q8TBF2, Q8VE98, Q92737, Q969P0, Q96NJ5, Q96NT3

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 15 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
protein folding641.4×5e-07
proteasome-mediated ubiquitin-dependent protein catabolic process517.4×4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance89
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3668 predictions. Top by Δscore:

VariantEffectΔscore
13:69711179:T:Adonor_gain1.0000
13:69740388:A:ACdonor_gain1.0000
13:69740389:C:CCdonor_gain1.0000
13:69740389:CTTA:Cdonor_gain1.0000
13:69740390:TTAC:Tdonor_loss1.0000
13:69740391:TACT:Tdonor_loss1.0000
13:69740392:A:ACdonor_gain1.0000
13:69740392:A:Tdonor_loss1.0000
13:69740393:C:CTdonor_gain1.0000
13:69740393:CT:Cdonor_gain1.0000
13:69740393:CTT:Cdonor_gain1.0000
13:69740393:CTTG:Cdonor_gain1.0000
13:69740556:CCTAA:Cacceptor_loss1.0000
13:69740557:CTA:Cacceptor_loss1.0000
13:69796732:TCTTA:Tdonor_loss1.0000
13:69796733:CTTAC:Cdonor_loss1.0000
13:69796734:TTAC:Tdonor_loss1.0000
13:69796735:TACC:Tdonor_loss1.0000
13:69796736:A:Cdonor_loss1.0000
13:69796737:C:Tdonor_loss1.0000
13:69796739:TAG:Tdonor_gain1.0000
13:69796740:AGA:Adonor_gain1.0000
13:69796960:CTC:Cacceptor_gain1.0000
13:69839158:AATAT:Aacceptor_gain1.0000
13:69839159:ATAT:Aacceptor_gain1.0000
13:69839160:TAT:Tacceptor_gain1.0000
13:69839161:AT:Aacceptor_gain1.0000
13:69839163:C:CCacceptor_gain1.0000
13:69839164:T:Aacceptor_loss1.0000
13:69859422:C:CAdonor_gain1.0000

AlphaMissense

4919 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:69701738:T:AR737S1.000
13:69701738:T:GR737S1.000
13:69707631:C:AW727C1.000
13:69707631:C:GW727C1.000
13:69707632:C:GW727S1.000
13:69707633:A:GW727R1.000
13:69707633:A:TW727R1.000
13:69707654:A:CY720D1.000
13:69707692:C:TG707D1.000
13:69707693:C:GG707R1.000
13:69707695:C:TG706D1.000
13:69707774:A:GW680R1.000
13:69707774:A:TW680R1.000
13:69707795:A:CY673D1.000
13:69719423:C:TG654D1.000
13:69719426:C:TG653E1.000
13:69719473:T:AR637S1.000
13:69719473:T:GR637S1.000
13:69719503:C:AW627C1.000
13:69719503:C:GW627C1.000
13:69719504:C:GW627S1.000
13:69719505:A:GW627R1.000
13:69719505:A:TW627R1.000
13:69719561:C:GR608P1.000
13:69719564:C:AG607V1.000
13:69719564:C:TG607D1.000
13:69719565:C:GG607R1.000
13:69719567:C:AG606V1.000
13:69719567:C:TG606E1.000
13:69719568:C:GG606R1.000

dbSNP variants (sampled 300 via entrez): RS1000004502 (13:69867951 A>G), RS1000008022 (13:69708585 A>T), RS1000018997 (13:69979339 T>G), RS1000041566 (13:69902547 A>G), RS1000047300 (13:69882062 T>A), RS1000047650 (13:70015928 C>T), RS1000049433 (13:70000505 T>C), RS1000049849 (13:69761405 G>C), RS1000055663 (13:69797577 G>A), RS1000062985 (13:69762773 C>A,T), RS1000076964 (13:69757371 C>T), RS1000080989 (13:69724044 G>A), RS1000084029 (13:69876306 T>C), RS1000084814 (13:69720161 G>A,C,T), RS1000090988 (13:69837481 A>G)

Disease associations

OMIM: gene MIM:605332 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

18 associations (top):

StudyTraitp-value
GCST000477_31Cognitive performance8.000000e-06
GCST001324_5Bilirubin levels7.000000e-06
GCST001651_85Response to amphetamines8.000000e-07
GCST001762_182Obesity-related traits2.000000e-06
GCST001762_519Obesity-related traits2.000000e-06
GCST002251_7Homeostasis model assessment of beta-cell function (dietary factor interaction)4.000000e-07
GCST002701_13Verbal declarative memory4.000000e-06
GCST003817_12Mortality in sepsis3.000000e-07
GCST003992_43Photic sneeze reflex6.000000e-15
GCST003995_14Tonsillectomy2.000000e-11
GCST005014_151Tonsillectomy2.000000e-11
GCST007576_72Chronotype2.000000e-12
GCST008181_16Spontaneous preterm birth without premature rupture of membranes9.000000e-06
GCST009236_1Asthma (time to childhood onset) in early life tobacco smoke exposure2.000000e-06
GCST009238_2Asthma (time to childhood onset) x early life tobacco smoke interaction4.000000e-08
GCST009543_1Cleft lip with or without cleft palate x maternal periconceptional vitamin use interaction (parent of origin effect)8.000000e-06
GCST010732_5Sensory peripheral neuropathy in microtubule targeting agent-treated breast cancer2.000000e-06
GCST011318_1Trigger finger2.000000e-10

EFO canonical traits (19, from GWAS)

EFO IDTrait name
EFO:0003926neuropsychological test
EFO:0004570bilirubin measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004469HOMA-B
EFO:0008111diet measurement
EFO:0004874memory performance
EFO:0006805word list delayed recall measurement
EFO:0004352mortality
EFO:0007887autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0007924tonsillectomy risk measurement
EFO:0008328chronotype measurement
EFO:0006917spontaneous preterm birth
EFO:0004847age at onset
EFO:0008361environmental tobacco smoke exposure measurement
EFO:0003959cleft lip
EFO:0005939parental genotype effect measurement
EFO:0009116vitamin supplement exposure measurement
EFO:0005260response to antimicrotubule agent
EFO:0010822stenosing tenosynovitis

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression2
Aflatoxin B1increases methylation, decreases methylation2
sodium arseniteaffects methylation1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, increases expression1
entinostatdecreases expression1
Vorinostatdecreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation1
Lipopolysaccharidesaffects cotreatment, increases expression1
Antirheumatic Agentsincreases expression1
Okadaic Aciddecreases expression1

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.