KLHDC3

gene
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Also known as PEAShPeasdJ20C7.3

Summary

KLHDC3 (kelch domain containing 3, HGNC:20704) is a protein-coding gene on chromosome 6p21.1, encoding Kelch domain-containing protein 3 (Q9BQ90). Substrate-recognition component of a Cul2-RING (CRL2) E3 ubiquitin-protein ligase complex of the DesCEND (destruction via C-end degrons) pathway, which recognizes a C-degron located at the extreme C terminus of target proteins, leading to their ubiquitination and degradation.

The protein encoded by this gene contains six repeated kelch motifs that are structurally similar to recombination activating gene 2, a protein involved in the activation of the V(D)J recombination. In mouse, this gene is found to be expressed specifically in testis. Its expression in pachytene spermatocytes is localized to cytoplasma and meiotic chromatin, suggesting that this gene may be involved in meiotic recombination.

Source: NCBI Gene 116138 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 43 total
  • MANE Select transcript: NM_057161

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20704
Approved symbolKLHDC3
Namekelch domain containing 3
Location6p21.1
Locus typegene with protein product
StatusApproved
AliasesPEAS, hPeas, dJ20C7.3
Ensembl geneENSG00000124702
Ensembl biotypeprotein_coding
OMIM611248
Entrez116138

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 25 protein_coding

ENST00000244670, ENST00000326974, ENST00000892793, ENST00000892794, ENST00000892795, ENST00000892796, ENST00000892797, ENST00000892798, ENST00000892799, ENST00000892800, ENST00000892801, ENST00000892802, ENST00000892803, ENST00000892804, ENST00000892805, ENST00000931056, ENST00000931057, ENST00000931058, ENST00000931059, ENST00000931060, ENST00000931061, ENST00000931062, ENST00000931063, ENST00000931064, ENST00000965771

RefSeq mRNA: 1 — MANE Select: NM_057161 NM_057161

CCDS: CCDS4880

Canonical transcript exons

ENST00000326974 — 11 exons

ExonStartEnd
ENSE000007515214301834343018556
ENSE000007515224301863343018719
ENSE000007515234301886343018971
ENSE000007515244301909243019165
ENSE000007515254301928843019366
ENSE000008500384301785343017968
ENSE000008500394301814543018216
ENSE000015499744301424943014348
ENSE000035551904301751943017695
ENSE000036503464301713443017346
ENSE000038472914302066743021294

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 98.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 71.7364 / max 433.3324, expressed in 1827 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
6784771.54331827
678480.102423
678500.077825
678490.01298

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453498.96gold quality
left testisUBERON:000453398.94gold quality
right frontal lobeUBERON:000281098.82gold quality
prefrontal cortexUBERON:000045198.51gold quality
cerebellar hemisphereUBERON:000224598.13gold quality
right hemisphere of cerebellumUBERON:001489098.13gold quality
cerebellar cortexUBERON:000212998.11gold quality
hindlimb stylopod muscleUBERON:000425298.09gold quality
Brodmann (1909) area 9UBERON:001354097.95gold quality
dorsolateral prefrontal cortexUBERON:000983497.86gold quality
triceps brachiiUBERON:000150997.83gold quality
nucleus accumbensUBERON:000188297.80gold quality
amygdalaUBERON:000187697.66gold quality
cingulate cortexUBERON:000302797.58gold quality
cerebellumUBERON:000203797.50gold quality
anterior cingulate cortexUBERON:000983597.48gold quality
caudate nucleusUBERON:000187397.45gold quality
putamenUBERON:000187497.43gold quality
frontal cortexUBERON:000187097.18gold quality
ganglionic eminenceUBERON:000402397.18gold quality
frontal lobeUBERON:001652597.18gold quality
cortical plateUBERON:000534397.15gold quality
apex of heartUBERON:000209897.10gold quality
testisUBERON:000047397.02gold quality
neocortexUBERON:000195096.97gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451196.94gold quality
ventricular zoneUBERON:000305396.91gold quality
muscle of legUBERON:000138396.82gold quality
frontal poleUBERON:000279596.82gold quality
gastrocnemiusUBERON:000138896.79gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting KLHDC3, 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-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-3163100.0077.238605
HSA-MIR-12118100.0065.881270
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-3689D100.0066.141181
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-477599.9875.006394
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-448799.9664.581252
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-629-3P99.8567.991875
HSA-MIR-3663-3P99.8470.39798
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-320299.6667.702737
HSA-MIR-4690-5P99.6566.24813

Literature-anchored findings (GeneRIF, showing 2)

  • cloned human and mouse Peas cDNAs (hPEAS/mPeas) and analyzed their tissue and stage-specific expressions; may be involved in meiotic recombination process (PMID:12606021)
  • CRL2(KLHDC3) mediates p14ARF N-terminal ubiquitylation degradation to promote non-small cell lung carcinoma progression. (PMID:35468939)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioklhdc3ENSDARG00000102772
mus_musculusKlhdc3ENSMUSG00000063576
rattus_norvegicusKlhdc3ENSRNOG00000017495

Paralogs (10): FBXO42 (ENSG00000037637), LZTR1 (ENSG00000099949), KLHDC4 (ENSG00000104731), HCFC2 (ENSG00000111727), KLHDC10 (ENSG00000128607), RABEPK (ENSG00000136933), KLHDC9 (ENSG00000162755), KLHDC2 (ENSG00000165516), HCFC1 (ENSG00000172534), KLHDC1 (ENSG00000197776)

Protein

Protein identifiers

Kelch domain-containing protein 3Q9BQ90 (reviewed: Q9BQ90)

Alternative names: Testis intracellular mediator protein

All UniProt accessions (2): Q9BQ90, F8W6A4

UniProt curated annotations — full annotation on UniProt →

Function. Substrate-recognition component of a Cul2-RING (CRL2) E3 ubiquitin-protein ligase complex of the DesCEND (destruction via C-end degrons) pathway, which recognizes a C-degron located at the extreme C terminus of target proteins, leading to their ubiquitination and degradation. The C-degron recognized by the DesCEND pathway is usually a motif of less than ten residues and can be present in full-length proteins, truncated proteins or proteolytically cleaved forms. The CRL2(KLHDC3) complex specifically recognizes proteins with a glycine (Gly) at the C-terminus, leading to their ubiquitination and degradation: recognizes the C-terminal -Arg-(Xaa)n-Arg-Gly, -Arg-(Xaa)n-Lys-Gly, and -Arg-(Xaa)n-Gln-Gly degrons. The CRL2(KLHDC3) complex mediates ubiquitination and degradation of truncated SELENOV and SEPHS2 selenoproteins produced by failed UGA/Sec decoding, which end with a glycine. May be involved in meiotic recombination process.

Subunit / interactions. Component of a CRL2(KLHDC3) complex, also named ECS(KLHDC3) complex, composed of CUL2, Elongin BC (ELOB and ELOC), RBX1 and substrate-specific adapter KLHDC3. May form oligomers as a KLHDC3-ELOB-ELOC complex; this interaction is likely autoinhibitory for the E3 ligase complex.

Subcellular location. Cytoplasm.

Pathway. Protein modification; protein ubiquitination.

RefSeq proteins (1): NP_476502* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006652Kelch_1Repeat
IPR015915Kelch-typ_b-propellerHomologous_superfamily
IPR052637KLHDC3-likeFamily

Pfam: PF01344, PF24681

UniProt features (46 total): strand 31, turn 7, repeat 5, helix 2, chain 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
9D1ZX-RAY DIFFRACTION1.88
9D1IX-RAY DIFFRACTION2
9D1YX-RAY DIFFRACTION2.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BQ90-F194.310.88

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-381038XBP1(S) activates chaperone genes
R-HSA-2262752Cellular responses to stress
R-HSA-381070IRE1alpha activates chaperones
R-HSA-381119Unfolded Protein Response (UPR)
R-HSA-8953897Cellular responses to stimuli

MSigDB gene sets: 194 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, MODULE_52, REACTOME_UNFOLDED_PROTEIN_RESPONSE_UPR, TGCGCANK_UNKNOWN, ATACCTC_MIR202, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, GGGTGGRR_PAX4_03, GGAMTNNNNNTCCY_UNKNOWN, MODULE_66, MODULE_120, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_ORGANELLE_FISSION, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, HIF1_Q3

GO Biological Process (5): reciprocal meiotic recombination (GO:0007131), protein ubiquitination (GO:0016567), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), ubiquitin-dependent protein catabolic process via the C-end degron rule pathway (GO:0140627), meiotic cell cycle (GO:0051321)

GO Molecular Function (3): chromatin binding (GO:0003682), ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), Cul2-RING ubiquitin ligase complex (GO:0031462)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
IRE1alpha activates chaperones1
Cellular responses to stimuli1
Unfolded Protein Response (UPR)1
Cellular responses to stress1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
binding2
meiosis I1
reciprocal homologous recombination1
meiotic cell cycle process1
protein modification by small protein conjugation1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
proteasome-mediated ubiquitin-dependent protein catabolic process1
cell cycle1
sexual reproduction1
reproductive process1
meiotic nuclear division1
enzyme-substrate adaptor activity1
chromosome1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
cullin-RING ubiquitin ligase complex1

Protein interactions and networks

STRING

796 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KLHDC3MEA1Q16626942
KLHDC3PPP2R5DQ14738937
KLHDC3SELENOSQ9BQE4557
KLHDC3APPBP2Q92624516
KLHDC3SELENOKQ9Y6D0510
KLHDC3SEPHS2Q99611499
KLHDC3SPATA4Q8NEY3471
KLHDC3SELENOVP59797470
KLHDC3PLAAT5Q96KN8467
KLHDC3CUL3Q13618463
KLHDC3RAG2P55895460
KLHDC3PRAMEF6Q5VXH4445
KLHDC3FEM1CQ96JP0441
KLHDC3SFI1A8K8P3439
KLHDC3PHKG2P11800431

IntAct

69 interactions, top by confidence:

ABTypeScore
CUL2VHLpsi-mi:“MI:0914”(association)0.940
EAF1ELL2psi-mi:“MI:0914”(association)0.840
KLHDC3CUL2psi-mi:“MI:0914”(association)0.770
KLHDC3CUL2psi-mi:“MI:0915”(physical association)0.770
CUL2COPS2psi-mi:“MI:0914”(association)0.640
CUL5SOCS7psi-mi:“MI:0914”(association)0.640
CHCHD4SSNA1psi-mi:“MI:0914”(association)0.640
GLMNFKBP5psi-mi:“MI:0914”(association)0.640
USP10ANKRD28psi-mi:“MI:0914”(association)0.610
WDR55PES1psi-mi:“MI:0914”(association)0.530
GLMNCUL1psi-mi:“MI:0914”(association)0.530
SLC31A1C2orf72psi-mi:“MI:0914”(association)0.530
VSIG4TCAF2psi-mi:“MI:0914”(association)0.530
KLHDC3DPYSL4psi-mi:“MI:0914”(association)0.530
IMPDH1BCAT2psi-mi:“MI:0914”(association)0.530
SUV39H1MAGEC1psi-mi:“MI:0914”(association)0.530
MISPOBSL1psi-mi:“MI:0914”(association)0.530
THOC3CLUHpsi-mi:“MI:0914”(association)0.530
G3BP2NUP214psi-mi:“MI:0914”(association)0.530
CHCHD4ENSApsi-mi:“MI:0914”(association)0.530
KLHDC3CLUHpsi-mi:“MI:0914”(association)0.530
POP7RPP40psi-mi:“MI:0914”(association)0.530
ZSCAN9SCAND1psi-mi:“MI:0914”(association)0.530
CSNK1EZSWIM8psi-mi:“MI:0914”(association)0.530

BioGRID (167): KLHDC3 (Affinity Capture-RNA), KLHDC3 (Affinity Capture-RNA), KLHDC3 (Affinity Capture-RNA), KLHDC3 (Affinity Capture-MS), KLHDC3 (Affinity Capture-MS), COPS2 (Affinity Capture-MS), RPP25L (Affinity Capture-MS), CUL2 (Affinity Capture-MS), COPS6 (Affinity Capture-MS), BRAP (Affinity Capture-MS), DPYSL5 (Affinity Capture-MS), NEDD8 (Affinity Capture-MS), USP10 (Affinity Capture-MS), NUDCD3 (Affinity Capture-MS), TSPYL4 (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8Q1W5, A2AAX3, A4IF63, A6QQY2, D3ZA50, D3ZQG6, F7H9X2, G3X9X1, O95199, P28575, P57790, Q14145, Q28DE7, Q2T9Z7, Q2WGJ6, Q56A24, Q58CV6, Q59H18, Q5BK60, Q5GIG6, Q5R774, Q5RCZ7, Q5RDY3, Q5U3Y0, Q5U580, Q5ZJU2, Q5ZLD3, Q684M4, Q6AYI2, Q6P798, Q6TFL4, Q6ZPT1, Q7TQP6, Q80TF4, Q80YG3, Q8BRG6, Q8BSF5, Q8IY47, Q8N7A1, Q8VEM9

Diamond homologs: A8JAM0, D3ZN95, G5EC23, P38853, P51610, P51611, Q10AZ7, Q4V8F4, Q53EP0, Q5RDA9, Q5RKG2, Q61191, Q6AYI2, Q6NWW9, Q6P3S6, Q7M3S9, Q8H4D4, Q8VEM9, Q93XW5, Q9BQ90, Q9D968, Q9V4C8, Q9Y5Z7, Q5EA50, Q86L99, Q94BT6, Q9C8K7, Q58CV6, Q5R4Q7, Q8N653, Q8W4K1, B8A5G9, C6A5A3, D3BT31, E3KWE1, F7A355, G1FNI6, O58523, O58796, P53177

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 88 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.

Reactome pathways:

PathwayPartnersFoldFDR
Neddylation97.5×8e-04

GO biological processes:

GO termPartnersFoldFDR
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process523.4×1e-03
proteasome-mediated ubiquitin-dependent protein catabolic process95.9×4e-03
protein ubiquitination105.2×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance29
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1184 predictions. Top by Δscore:

VariantEffectΔscore
6:43017517:A:AGacceptor_gain1.0000
6:43017518:G:GGacceptor_gain1.0000
6:43017518:GT:Gacceptor_gain1.0000
6:43017518:GTGT:Gacceptor_gain1.0000
6:43017518:GTGTC:Gacceptor_gain1.0000
6:43017691:CGTCA:Cdonor_loss1.0000
6:43017692:GTCA:Gdonor_gain1.0000
6:43017693:TCA:Tdonor_gain1.0000
6:43017694:CAGT:Cdonor_loss1.0000
6:43017695:AGT:Adonor_loss1.0000
6:43017696:G:GGdonor_gain1.0000
6:43017697:T:Adonor_loss1.0000
6:43017698:GAGT:Gdonor_loss1.0000
6:43017699:AGTA:Adonor_loss1.0000
6:43017700:G:GGdonor_gain1.0000
6:43017965:GCAG:Gdonor_gain1.0000
6:43018553:GCCT:Gdonor_gain1.0000
6:43018557:G:GGdonor_gain1.0000
6:43018627:TTCCA:Tacceptor_loss1.0000
6:43018628:TCCA:Tacceptor_loss1.0000
6:43018629:CCAGT:Cacceptor_loss1.0000
6:43018630:CAGTT:Cacceptor_loss1.0000
6:43018631:A:ACacceptor_loss1.0000
6:43018631:A:AGacceptor_gain1.0000
6:43018631:AGTT:Aacceptor_gain1.0000
6:43018631:AGTTG:Aacceptor_gain1.0000
6:43018632:G:GGacceptor_gain1.0000
6:43018632:GT:Gacceptor_gain1.0000
6:43018632:GTT:Gacceptor_gain1.0000
6:43018632:GTTG:Gacceptor_gain1.0000

AlphaMissense

2516 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:43017202:T:AW4R1.000
6:43017202:T:CW4R1.000
6:43017227:C:AP12H1.000
6:43017233:G:CR14T1.000
6:43017233:G:TR14M1.000
6:43017234:G:CR14S1.000
6:43017234:G:TR14S1.000
6:43017238:A:GN16D1.000
6:43017240:C:AN16K1.000
6:43017240:C:GN16K1.000
6:43017241:C:GH17D1.000
6:43017242:A:GH17R1.000
6:43017247:G:CA19P1.000
6:43017248:C:AA19E1.000
6:43017280:G:AG30R1.000
6:43017280:G:CG30R1.000
6:43017280:G:TG30W1.000
6:43017281:G:AG30E1.000
6:43017281:G:TG30V1.000
6:43017283:G:CG31R1.000
6:43017283:G:TG31C1.000
6:43017284:G:AG31D1.000
6:43017284:G:TG31V1.000
6:43017530:T:AW56R1.000
6:43017530:T:CW56R1.000
6:43017531:G:CW56S1.000
6:43017532:G:CW56C1.000
6:43017532:G:TW56C1.000
6:43017585:C:AP74H1.000
6:43017593:C:AR77S1.000

dbSNP variants (sampled 300 via entrez): RS1000201066 (6:43015228 C>T), RS1001039061 (6:43013797 T>A), RS1001151588 (6:43013978 A>C,G), RS1001268356 (6:43014282 C>T), RS1001475564 (6:43021236 C>T), RS1001819790 (6:43021489 T>C), RS1002256055 (6:43017173 T>C), RS1002910460 (6:43021225 C>T), RS1003230003 (6:43015408 AG>A), RS1003259398 (6:43015942 T>TG), RS1003540136 (6:43021087 C>G,T), RS1003560736 (6:43016394 T>G), RS1003611761 (6:43016047 T>A), RS1003920083 (6:43020006 T>C), RS1004138131 (6:43019755 A>T)

Disease associations

OMIM: gene MIM:611248 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance2
Cyclosporinedecreases expression2
aristolochic acid Iincreases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aaffects expression1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
potassium chromate(VI)affects cotreatment, decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1
Acetaminophendecreases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Coumestrolaffects cotreatment, increases expression1
Doxorubicinincreases expression1
Manganesedecreases expression, increases abundance, affects cotreatment1
Plant Extractsaffects cotreatment, increases expression1
Plant Oilsdecreases expression1
Selenomethionineaffects expression1
Smokedecreases expression1
Thiramdecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Cadmium Chloridedecreases expression1
tert-Butylhydroperoxidedecreases expression1

Cellosaurus cell lines

4 cell lines: 3 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2ZVAbcam HEK293T KLHDC3 KOTransformed cell lineFemale
CVCL_E2AIHAP1 KLHDC3 (-) 1Cancer cell lineMale
CVCL_E2AJHAP1 KLHDC3 (-) 2Cancer cell lineMale
CVCL_E2AKHAP1 KLHDC3 (-) 3Cancer cell lineMale

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.