KNDC1

gene
On this page

Also known as KIAA1768bB439H18.3FLJ25027Very-KINDv-KIND

Summary

KNDC1 (kinase non-catalytic C-lobe domain containing 1, HGNC:29374) is a protein-coding gene on chromosome 10q26.3, encoding Kinase non-catalytic C-lobe domain-containing protein 1 (Q76NI1). RAS-Guanine nucleotide exchange factor (GEF) that controls the negative regulation of neuronal dendrite growth by mediating a signaling pathway linking RAS and MAP2.

The protein encoded by this gene is a Ras guanine nucleotide exchange factor that appears to negatively regulate dendritic growth in the brain. Knockdown of this gene in senescent umbilical vein endothelial cells partially reversed the senescence, showing that this gene could potentially be targeted by anti-aging therapies.

Source: NCBI Gene 85442 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 385 total — 1 pathogenic
  • MANE Select transcript: NM_152643

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29374
Approved symbolKNDC1
Namekinase non-catalytic C-lobe domain containing 1
Location10q26.3
Locus typegene with protein product
StatusApproved
AliasesKIAA1768, bB439H18.3, FLJ25027, Very-KIND, v-KIND
Ensembl geneENSG00000171798
Ensembl biotypeprotein_coding
OMIM616237
Entrez85442

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 12 protein_coding, 9 nonsense_mediated_decay, 5 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000304613, ENST00000368571, ENST00000478074, ENST00000485110, ENST00000530127, ENST00000682119, ENST00000682309, ENST00000682310, ENST00000682399, ENST00000682765, ENST00000683144, ENST00000683171, ENST00000683259, ENST00000683646, ENST00000683920, ENST00000684081, ENST00000684098, ENST00000684127, ENST00000684244, ENST00000684248, ENST00000684271, ENST00000684403, ENST00000684739, ENST00000684767, ENST00000919719, ENST00000946347, ENST00000946348

RefSeq mRNA: 4 — MANE Select: NM_152643 NM_001347864, NM_001347865, NM_001347866, NM_152643

CCDS: CCDS7674, CCDS91388, CCDS91389, CCDS91390

Canonical transcript exons

ENST00000304613 — 30 exons

ExonStartEnd
ENSE00001096949133219031133219090
ENSE00001096954133219955133220112
ENSE00001152990133224659133226412
ENSE00001152998133206685133206778
ENSE00001153056133188539133188653
ENSE00001323571133206856133206953
ENSE00001356846133189598133189669
ENSE00001409509133207137133207351
ENSE00001647099133218831133218953
ENSE00001669459133211422133211569
ENSE00001675307133213645133213727
ENSE00001680208133212716133212922
ENSE00001697341133213972133214122
ENSE00001801667133211679133211858
ENSE00001949770133160219133160569
ENSE00003243477133201501133201898
ENSE00003283928133198578133199266
ENSE00003313627133189752133189813
ENSE00003326058133200375133200460
ENSE00003342425133183344133183490
ENSE00003350272133185974133186674
ENSE00003369482133197058133197135
ENSE00003392339133195663133195821
ENSE00003401353133198337133198499
ENSE00003401489133210611133210724
ENSE00003421125133183872133183989
ENSE00003431146133199458133199602
ENSE00003437093133197675133197768
ENSE00003526294133168254133168312
ENSE00003691247133167381133167579

Expression profiles

Bgee: expression breadth ubiquitous, 190 present calls, max score 94.08.

FANTOM5 (CAGE): breadth broad, TPM avg 2.6135 / max 101.4175, expressed in 574 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1077501.7222497
1077510.7355244
1077490.155884

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489094.08gold quality
cerebellar hemisphereUBERON:000224593.69gold quality
cerebellar cortexUBERON:000212993.63gold quality
lateral nuclear group of thalamusUBERON:000273693.43gold quality
right uterine tubeUBERON:000130293.28gold quality
cerebellumUBERON:000203793.12gold quality
right frontal lobeUBERON:000281092.46gold quality
Brodmann (1909) area 9UBERON:001354090.49gold quality
pituitary glandUBERON:000000790.33gold quality
left adrenal gland cortexUBERON:003582590.24gold quality
anterior cingulate cortexUBERON:000983590.12gold quality
dorsolateral prefrontal cortexUBERON:000983490.10gold quality
left adrenal glandUBERON:000123489.76gold quality
bronchial epithelial cellCL:000232889.72gold quality
amygdalaUBERON:000187689.58gold quality
primary visual cortexUBERON:000243689.58gold quality
right adrenal glandUBERON:000123389.55gold quality
adenohypophysisUBERON:000219689.46gold quality
frontal cortexUBERON:000187089.15gold quality
entorhinal cortexUBERON:000272889.10gold quality
temporal lobeUBERON:000187189.03gold quality
cerebellar vermisUBERON:000472089.01gold quality
neocortexUBERON:000195088.89gold quality
bronchusUBERON:000218588.69gold quality
postcentral gyrusUBERON:000258188.68gold quality
right adrenal gland cortexUBERON:003582788.45gold quality
cerebral cortexUBERON:000095688.40gold quality
adrenal cortexUBERON:000123588.38gold quality
hypothalamusUBERON:000189888.38gold quality
superior frontal gyrusUBERON:000266188.38gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting KNDC1, 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-6867-5P100.0082.213464
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-545-3P99.9570.742783
HSA-MIR-153-5P99.8973.866317
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-444799.8567.812900
HSA-MIR-1213099.7565.47452
HSA-MIR-6762-3P99.6666.941188
HSA-MIR-447299.5666.081478
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-361299.4566.021333
HSA-MIR-65099.4565.771309
HSA-MIR-3692-5P99.2967.041421
HSA-MIR-6852-5P99.1766.692073
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-429299.1665.571767
HSA-MIR-4763-3P99.1067.832649
HSA-MIR-4650-3P99.0168.391062
HSA-MIR-474499.0169.911581
HSA-MIR-445198.8268.171455
HSA-MIR-38498.7167.341229
HSA-MIR-6830-3P98.6268.071760
HSA-MIR-444398.0266.251928
HSA-MIR-63797.9164.051517
HSA-MIR-7111-3P97.8066.751467
HSA-MIR-299-3P97.7366.67773
HSA-MIR-4714-5P97.0467.76955
HSA-MIR-7847-3P96.6364.58952

Literature-anchored findings (GeneRIF, showing 2)

  • KNDC1 knockdown promoted HUVEC proliferation via the extracellular signal-regulated kinase signaling pathway and delayed HUVEC senescence by inhibiting the p53-p21-p16 transduction cascade. (PMID:24788352)
  • The results demonstrated that KNDC1 overexpression possibly inhibited HUVEC activity and function and promoted HUVEC senescence. Mechanistic studies demonstrated that KNDC1 triggered a p53ROS positive feedback loop, which serves a crucial role in regulating senescence. (PMID:29568929)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioENSDARG00000116483
mus_musculusKndc1ENSMUSG00000066129
rattus_norvegicusKndc1ENSRNOG00000027240

Protein

Protein identifiers

Kinase non-catalytic C-lobe domain-containing protein 1Q76NI1 (reviewed: Q76NI1)

Alternative names: Cerebral protein 9, Protein very KIND, Ras-GEF domain-containing family member 2

All UniProt accessions (14): Q76NI1, A0A7I2PM36, A0A804HHZ0, A0A804HI19, A0A804HI34, A0A804HID6, A0A804HIF7, A0A804HIR2, A0A804HIR7, A0A804HIZ4, A0A804HJH2, A0A804HKE4, A0A804HKF6, A0A804HKW7

UniProt curated annotations — full annotation on UniProt →

Function. RAS-Guanine nucleotide exchange factor (GEF) that controls the negative regulation of neuronal dendrite growth by mediating a signaling pathway linking RAS and MAP2. May be involved in cellular senescence.

Subunit / interactions. Interacts (via KIND2) with MAP2; the interaction enhances MAP2 phosphorylation and localizes KNDC1 to dendrites.

Subcellular location. Cell projection. Dendrite. Perikaryon.

Tissue specificity. Expressed specifically in the cerebral cortex.

Isoforms (2)

UniProt IDNamesCanonical?
Q76NI1-11yes
Q76NI1-42

RefSeq proteins (4): NP_001334793, NP_001334794, NP_001334795, NP_689856* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000651Ras-like_Gua-exchang_fac_NDomain
IPR001895RASGEF_cat_domDomain
IPR011009Kinase-like_dom_sfHomologous_superfamily
IPR011019KIND_domDomain
IPR023578Ras_GEF_dom_sfHomologous_superfamily
IPR029899KNDC1Family
IPR036964RASGEF_cat_dom_sfHomologous_superfamily

Pfam: PF00617, PF00618, PF16474

UniProt features (38 total): compositionally biased region 10, sequence conflict 10, sequence variant 5, domain 4, region of interest 4, splice variant 2, chain 1, modified residue 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q76NI1-F161.250.22

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 964

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): GOBP_DENDRITE_DEVELOPMENT, GOBP_HINDBRAIN_DEVELOPMENT, GOBP_METENCEPHALON_DEVELOPMENT, GOBP_REGULATION_OF_DENDRITE_MORPHOGENESIS, GOBP_CEREBELLAR_CORTEX_MORPHOGENESIS, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_CEREBELLAR_GRANULAR_LAYER_DEVELOPMENT, GOBP_CEREBELLAR_CORTEX_DEVELOPMENT, GOBP_DENDRITE_MORPHOGENESIS, GOBP_CELL_DIFFERENTIATION_IN_HINDBRAIN, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_HEAD_DEVELOPMENT, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT

GO Biological Process (4): small GTPase-mediated signal transduction (GO:0007264), cerebellar granule cell differentiation (GO:0021707), regulation of dendrite morphogenesis (GO:0048814), regulation of dendrite development (GO:0050773)

GO Molecular Function (1): guanyl-nucleotide exchange factor activity (GO:0005085)

GO Cellular Component (5): dendrite (GO:0030425), guanyl-nucleotide exchange factor complex (GO:0032045), neuronal cell body (GO:0043025), perikaryon (GO:0043204), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
intracellular signaling cassette1
cell differentiation in hindbrain1
cerebellar granular layer formation1
central nervous system neuron differentiation1
glutamatergic neuron differentiation1
regulation of anatomical structure morphogenesis1
dendrite morphogenesis1
regulation of dendrite development1
regulation of neuron projection development1
dendrite development1
regulation of developmental process1
GTP binding1
GDP binding1
GTPase regulator activity1
neuron projection1
dendritic tree1
intracellular protein-containing complex1
somatodendritic compartment1
cell body1
neuronal cell body1

Protein interactions and networks

STRING

776 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KNDC1ADGRA1Q86SQ6665
KNDC1CDH24Q86UP0579
KNDC1ZSCAN29Q8IWY8518
KNDC1CDHR2Q9BYE9518
KNDC1ITM2CQ9NQX7513
KNDC1ZSCAN20P17040490
KNDC1LRRC71Q8N4P6480
KNDC1CDH18Q13634446
KNDC1SLC36A4Q6YBV0434
KNDC1PTPRTO14522429
KNDC1FRMPD2Q68DX3419
KNDC1GPR183P32249386
KNDC1VENTXO95231376
KNDC1SLC15A1P46059368
KNDC1SHISAL2AQ6UWV7365

IntAct

9 interactions, top by confidence:

ABTypeScore
P/VIRS4psi-mi:“MI:0914”(association)0.530
KNDC1LMNApsi-mi:“MI:0915”(physical association)0.400
KNDC1ATP5POpsi-mi:“MI:0915”(physical association)0.400
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
Prdm16ESYT2psi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
MYCPDZD2psi-mi:“MI:0914”(association)0.350
KNDC1ASAP2psi-mi:“MI:0914”(association)0.350

BioGRID (26): KNDC1 (Affinity Capture-MS), KNDC1 (Affinity Capture-RNA), KNDC1 (Affinity Capture-MS), KNDC1 (Proximity Label-MS), KNDC1 (Proximity Label-MS), KNDC1 (Affinity Capture-MS), ANAPC4 (Affinity Capture-MS), DYRK1A (Affinity Capture-MS), EPDR1 (Affinity Capture-MS), NDUFS1 (Affinity Capture-MS), PPP2R5B (Affinity Capture-MS), PPP2R5E (Affinity Capture-MS), PPP2R5A (Affinity Capture-MS), AHCYL2 (Affinity Capture-MS), DCAF7 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RRK4, A0A1W2PPE3, A0A1W2PR82, A0A2Z4LIS9, A2VE02, A4D1S0, A5PKC7, A5PL33, A6H7B4, A6NEL2, A6QP24, A6QPM6, A8MTW9, A8MYA2, D3ZAQ5, D4AAA5, E7EW31, O75474, O75638, O89113, O94850, P0C7X2, P14652, P50617, P70339, Q2KIS6, Q3UN58, Q5JPB2, Q5VZ46, Q6GQX2, Q6NZ36, Q6ZSJ8, Q6ZW13, Q76NI1, Q7TNS8, Q80TS7, Q86UU5, Q8IWN7, Q8N6K4, Q8N944

Diamond homologs: Q0KK55, Q76NI1, Q8IS18

SIGNOR signaling

1 interactions.

AEffectBMechanism
KNDC1“up-regulates activity”MAP2phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance324
Likely benign34
Benign8

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2574693GRCh37/hg19 10q26.13-26.3(chr10:123477898-135427143)Pathogenic

SpliceAI

6779 predictions. Top by Δscore:

VariantEffectΔscore
10:133160566:CGAGG:Cdonor_loss1.0000
10:133160567:GAG:Gdonor_gain1.0000
10:133160567:GAGGT:Gdonor_loss1.0000
10:133160568:AGGTG:Adonor_loss1.0000
10:133160569:GGTG:Gdonor_loss1.0000
10:133160570:G:Cdonor_loss1.0000
10:133160570:G:GGdonor_gain1.0000
10:133160571:T:Gdonor_loss1.0000
10:133167577:GCG:Gdonor_gain1.0000
10:133168252:A:Gacceptor_gain1.0000
10:133168253:G:GGacceptor_gain1.0000
10:133183338:CCACA:Cacceptor_loss1.0000
10:133183341:CA:Cacceptor_loss1.0000
10:133183342:A:AGacceptor_gain1.0000
10:133183342:A:Cacceptor_loss1.0000
10:133183343:G:GGacceptor_gain1.0000
10:133183343:GGC:Gacceptor_gain1.0000
10:133183343:GGCGC:Gacceptor_gain1.0000
10:133183488:GAG:Gdonor_gain1.0000
10:133183488:GAGGT:Gdonor_loss1.0000
10:133183489:AGG:Adonor_loss1.0000
10:133183490:GGT:Gdonor_loss1.0000
10:133183491:G:GGdonor_gain1.0000
10:133183491:GT:Gdonor_loss1.0000
10:133188537:AGTG:Aacceptor_gain1.0000
10:133188538:GTGG:Gacceptor_gain1.0000
10:133198497:CAGGT:Cdonor_loss1.0000
10:133198498:AGGT:Adonor_loss1.0000
10:133198501:T:Adonor_loss1.0000
10:133199450:A:AGacceptor_gain1.0000

AlphaMissense

11365 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:133167538:T:CF87S0.999
10:133220099:T:AW1669R0.999
10:133220099:T:CW1669R0.999
10:133206752:T:CL1152P0.998
10:133211468:A:CS1319R0.998
10:133211470:C:AS1319R0.998
10:133211470:C:GS1319R0.998
10:133211489:T:AW1326R0.998
10:133211489:T:CW1326R0.998
10:133214084:T:AW1547R0.998
10:133214084:T:CW1547R0.998
10:133214093:G:CA1550P0.998
10:133219077:T:CL1616P0.998
10:133167532:T:CL85P0.997
10:133206739:T:CF1148L0.997
10:133206741:C:AF1148L0.997
10:133206741:C:GF1148L0.997
10:133207330:T:CL1258P0.997
10:133167562:T:CF95S0.996
10:133183372:T:CL130P0.996
10:133199538:T:AW947R0.996
10:133199538:T:CW947R0.996
10:133199563:T:CL955P0.996
10:133206886:T:CL1171P0.996
10:133212906:T:CL1476P0.996
10:133167444:T:AW56R0.995
10:133167444:T:CW56R0.995
10:133167453:T:CC59R0.995
10:133167517:T:AI80N0.995
10:133183362:G:TG127W0.995

dbSNP variants (sampled 300 via entrez): RS1000015295 (10:133170226 C>T), RS1000089431 (10:133178596 G>A), RS1000096301 (10:133161899 G>A,T), RS1000126885 (10:133200868 T>C), RS1000167809 (10:133196359 C>T), RS1000177906 (10:133211126 G>A), RS1000234290 (10:133204496 C>T), RS1000268903 (10:133165322 G>A), RS1000318661 (10:133192342 G>C,T), RS1000375060 (10:133173731 C>T), RS1000391039 (10:133200373 AGCACGGC>A), RS1000411933 (10:133200702 G>A), RS1000453167 (10:133216860 G>A), RS1000480869 (10:133189067 G>A,T), RS1000494824 (10:133168763 G>T)

Disease associations

OMIM: gene MIM:616237 | disease phenotypes: MIM:609625

GenCC curated gene-disease

Mondo (2): breast ductal adenocarcinoma (MONDO:0005590), distal 10q deletion syndrome (MONDO:0012315)

Orphanet (1): Distal deletion 10q syndrome (Orphanet:96148)

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST008512_29Multisite chronic pain4.000000e-08
GCST009514_3Recurrence of mild malaria attacks8.000000e-07
GCST90000514_15Gastroesophageal reflux disease5.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0010100multisite chronic pain
EFO:0004952disease recurrence

MeSH disease descriptors (2)

DescriptorNameTree numbers
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390
C567182Chromosome 10q26 Deletion Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
mercuric bromidedecreases expression, affects cotreatment2
Benzo(a)pyreneaffects methylation, increases methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tobacco Smoke Pollutiondecreases methylation, decreases expression2
Valproic Acidincreases methylation, affects expression2
fluorene-9-bisphenoldecreases expression1
bisphenol Adecreases methylation1
ethyl-p-hydroxybenzoatedecreases expression1
sodium arseniteaffects binding, increases reaction1
butyraldehydedecreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2affects methylation1
CGP 52608increases reaction, affects binding1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
licochalcone Bdecreases expression1
bisphenol Sdecreases methylation1
jinfukangincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Acetaminophenincreases expression1
Air Pollutantsaffects methylation, increases abundance1
Cadmiumincreases abundance, decreases expression1
Copperaffects cotreatment, decreases expression1
Diazinonincreases methylation1
Diethylhexyl Phthalatedecreases expression1
Methapyrileneincreases methylation1
Silicon Dioxidedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03414970PHASE3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344PHASE2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999PHASE2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364PHASE1/PHASE2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855PHASE1/PHASE2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908EARLY_PHASE1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041EARLY_PHASE1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974Not specifiedACTIVE_NOT_RECRUITINGNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery