KATNAL1

gene
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Also known as MGC2599

Summary

KATNAL1 (katanin catalytic subunit A1 like 1, HGNC:28361) is a protein-coding gene on chromosome 13q12.3, encoding Katanin p60 ATPase-containing subunit A-like 1 (Q9BW62). Regulates microtubule dynamics in Sertoli cells, a process that is essential for spermiogenesis and male fertility.

Enables identical protein binding activity and microtubule severing ATPase activity. Involved in microtubule severing. Located in cytosol; microtubule cytoskeleton; and mitochondrion. Part of katanin complex.

Source: NCBI Gene 84056 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 77 total
  • MANE Select transcript: NM_032116

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28361
Approved symbolKATNAL1
Namekatanin catalytic subunit A1 like 1
Location13q12.3
Locus typegene with protein product
StatusApproved
AliasesMGC2599
Ensembl geneENSG00000102781
Ensembl biotypeprotein_coding
OMIM614764
Entrez84056

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 13 protein_coding, 1 retained_intron

ENST00000380615, ENST00000380617, ENST00000414289, ENST00000441394, ENST00000480854, ENST00000908521, ENST00000908522, ENST00000908523, ENST00000908524, ENST00000908525, ENST00000931886, ENST00000931887, ENST00000961620, ENST00000961621

RefSeq mRNA: 2 — MANE Select: NM_032116 NM_001014380, NM_032116

CCDS: CCDS31956

Canonical transcript exons

ENST00000380615 — 11 exons

ExonStartEnd
ENSE000006798543028006330280223
ENSE000006798603028361630283791
ENSE000013604823030733130307551
ENSE000014856353020263030208738
ENSE000015919273024095930241086
ENSE000016314933023046830230594
ENSE000016912973021031630210442
ENSE000017191163022741230227546
ENSE000017997813023131430231472
ENSE000018022883024046030240565
ENSE000021893163025544730255615

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 96.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3032 / max 215.3042, expressed in 1696 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1366243.39841207
1366251.81361125
1366221.7048852
1366230.8065490
1366260.5799341

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065596.49gold quality
oocyteCL:000002395.46gold quality
cardiac muscle of right atriumUBERON:000337995.16gold quality
left ventricle myocardiumUBERON:000656694.79gold quality
spermCL:000001992.98gold quality
Brodmann (1909) area 23UBERON:001355492.92gold quality
endothelial cellCL:000011592.81gold quality
calcaneal tendonUBERON:000370191.90gold quality
middle temporal gyrusUBERON:000277191.51gold quality
myocardiumUBERON:000234990.99gold quality
heart right ventricleUBERON:000208090.72gold quality
corpus callosumUBERON:000233689.36gold quality
tendonUBERON:000004389.33gold quality
postcentral gyrusUBERON:000258188.92gold quality
superior frontal gyrusUBERON:000266188.02gold quality
parietal lobeUBERON:000187287.89gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.45gold quality
entorhinal cortexUBERON:000272887.21gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.94gold quality
Brodmann (1909) area 46UBERON:000648386.78gold quality
ponsUBERON:000098886.77gold quality
saphenous veinUBERON:000731886.73gold quality
lateral nuclear group of thalamusUBERON:000273686.36gold quality
sural nerveUBERON:001548885.96gold quality
smooth muscle tissueUBERON:000113585.83gold quality
substantia nigra pars compactaUBERON:000196585.44gold quality
cortical plateUBERON:000534385.26gold quality
deciduaUBERON:000245085.13gold quality
ventricular zoneUBERON:000305384.71gold quality
parietal pleuraUBERON:000240084.68gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.46
E-CURD-10no239.46

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F4

miRNA regulators (miRDB)

250 targeting KATNAL1, 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-3613-3P100.0076.367965
HSA-MIR-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-574-5P100.0066.01989
HSA-MIR-8485100.0077.574731
HSA-MIR-4455100.0065.481587
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548AW99.9972.573559
HSA-MIR-450099.9972.722367
HSA-MIR-548N99.9871.944170
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-569699.9872.364487
HSA-MIR-314899.9775.066478
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-365899.9673.874379
HSA-MIR-570-3P99.9672.414910
HSA-MIR-9-3P99.9670.882068
HSA-MIR-55999.9572.283609

Literature-anchored findings (GeneRIF, showing 4)

  • KL1-mediated microtubule severing is utilized to generate microtubule seeds within the poles and loss of this activity alters the normal balance of motor-generated forces that determine spindle length. (PMID:20519956)
  • microdeletion 13q12.3 represents a novel clinically recognizable condition and that the microtubule severing gene KATNAL1 and the chromatin-associated gene HMGB1 are candidate genes for intellectual disability inherited in an autosomal dominant pattern. (PMID:24664804)
  • KATNAL1 gene sequence variants are not associated with azoospermia. (PMID:24913027)
  • Common genetic variation in KATNAL1 non-coding regions is involved in the susceptibility to severe phenotypes of male infertility. (PMID:35752927)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_reriokatnal1ENSDARG00000099156
mus_musculusKatnal1ENSMUSG00000041298
rattus_norvegicusKatnal1ENSRNOG00000047618
drosophila_melanogasterFignFBGN0031519
drosophila_melanogasterkat-60L1FBGN0037375
drosophila_melanogasterKat60FBGN0040208
caenorhabditis_elegansmei-1WBGENE00003183
caenorhabditis_elegansWBGENE00017981

Paralogs (9): SPAST (ENSG00000021574), VPS4B (ENSG00000119541), FIGNL1 (ENSG00000132436), VPS4A (ENSG00000132612), ATAD1 (ENSG00000138138), KATNAL2 (ENSG00000167216), FIGN (ENSG00000182263), KATNA1 (ENSG00000186625), FIGNL2 (ENSG00000261308)

Protein

Protein identifiers

Katanin p60 ATPase-containing subunit A-like 1Q9BW62 (reviewed: Q9BW62)

Alternative names: p60 katanin-like 1

All UniProt accessions (3): Q9BW62, A2A3H2, Q5T558

UniProt curated annotations — full annotation on UniProt →

Function. Regulates microtubule dynamics in Sertoli cells, a process that is essential for spermiogenesis and male fertility. Severs microtubules in an ATP-dependent manner, promoting rapid reorganization of cellular microtubule arrays. Has microtubule-severing activity in vitro.

Subunit / interactions. Interacts with KATNB1 and KATNBL1.

Subcellular location. Cytoplasm. Cytoskeleton. Spindle pole. Spindle.

Tissue specificity. Expressed in testis, restricted to Sertoli cells (at protein level).

Similarity. Belongs to the AAA ATPase family. Katanin p60 subunit A1 subfamily. A-like 1 sub-subfamily.

RefSeq proteins (2): NP_001014402, NP_115492* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003593AAA+_ATPaseDomain
IPR003959ATPase_AAA_coreDomain
IPR003960ATPase_AAA_CSConserved_site
IPR015415Spast_Vps4_CDomain
IPR027417P-loop_NTPaseHomologous_superfamily
IPR028594Katnal1_chordatesFamily
IPR028596KATNA1Family
IPR041569AAA_lid_3Domain
IPR048611KATNA1_MITDomain
IPR048612KTNA1_AAA_domDomain
IPR050304MT-severing_AAA_ATPaseFamily

Pfam: PF00004, PF09336, PF17862, PF21126

Enzyme classification (BRENDA):

  • EC 5.6.1.1 — microtubule-severing ATPase (BRENDA: 21 organisms, 29 substrates, 57 inhibitors, 16 Km, 12 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
ATP0.0003–2.9416

UniProt features (34 total): helix 19, strand 6, compositionally biased region 3, modified residue 2, chain 1, region of interest 1, turn 1, binding site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6B5CX-RAY DIFFRACTION2.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BW62-F176.810.34

Functional residue map

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

Ligand- & substrate-binding residues (1): 248–255

Post-translational modifications (2): 1, 174

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 144 (showing top): GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, MODULE_255, MODULE_317, GOBP_MALE_GAMETE_GENERATION, GOCC_MICROTUBULE_ORGANIZING_CENTER, AACWWCAANK_UNKNOWN, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, GOCC_CENTROSOME, DOUGLAS_BMI1_TARGETS_DN, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, LEF1_Q6, RFX1_02, GOCC_SPINDLE, GOCC_MITOTIC_SPINDLE

GO Biological Process (4): spermatogenesis (GO:0007283), cytoplasmic microtubule organization (GO:0031122), microtubule severing (GO:0051013), microtubule cytoskeleton organization (GO:0000226)

GO Molecular Function (8): ATP binding (GO:0005524), microtubule binding (GO:0008017), microtubule severing ATPase activity (GO:0008568), ATP hydrolysis activity (GO:0016887), identical protein binding (GO:0042802), nucleotide binding (GO:0000166), protein binding (GO:0005515), isomerase activity (GO:0016853)

GO Cellular Component (11): spindle pole (GO:0000922), cytoplasm (GO:0005737), mitochondrion (GO:0005739), centrosome (GO:0005813), spindle (GO:0005819), cytosol (GO:0005829), microtubule (GO:0005874), katanin complex (GO:0008352), microtubule cytoskeleton (GO:0015630), mitotic spindle (GO:0072686), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
microtubule cytoskeleton organization3
cellular anatomical structure3
ATP-dependent activity2
spindle2
cytoplasm2
microtubule organizing center2
microtubule cytoskeleton2
intracellular membraneless organelle2
developmental process involved in reproduction1
male gamete generation1
supramolecular fiber organization1
cytoskeleton organization1
microtubule-based process1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
tubulin binding1
polypeptide conformation or assembly isomerase activity1
catalytic activity, acting on a protein1
microtubule destabilizing activity1
ribonucleoside triphosphate phosphatase activity1
protein binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
catalytic activity1
intracellular anatomical structure1
intracellular membrane-bounded organelle1
centriole1
polymeric cytoskeletal fiber1
microtubule associated complex1
cytoskeleton1

Protein interactions and networks

STRING

1801 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KATNAL1KATNB1Q9BVA0758
KATNAL1KATNBL1Q9H079577
KATNAL1NAA35Q5VZE5459
KATNAL1RELAQ04206406
KATNAL1KATNIPO60303399
KATNAL1KIF18AQ8NI77389
KATNAL1TEX26Q8N6G2381
KATNAL1USPL1Q5W0Q7365
KATNAL1SSH2Q76I76365
KATNAL1TUBGCP3Q96CW5354
KATNAL1TNS1Q9HBL0353
KATNAL1HTR2BP41595353
KATNAL1HERC5Q9UII4353
KATNAL1LUZP1Q86V48353
KATNAL1ZNHIT2Q9UHR6353
KATNAL1ARHGAP32A7KAX9353
KATNAL1ENTHD1Q8IYW4353
KATNAL1KIF15Q9NS87353
KATNAL1PRDM10Q9NQV6353
KATNAL1CNTNAP2Q9UHC6353

IntAct

124 interactions, top by confidence:

ABTypeScore
KATNAL1KATNBL1psi-mi:“MI:0915”(physical association)0.880
KATNBL1KATNAL1psi-mi:“MI:0915”(physical association)0.880
KATNAL1CEP57L1psi-mi:“MI:0915”(physical association)0.720
KLC4KATNAL1psi-mi:“MI:0915”(physical association)0.720
KATNAL1AIRIMpsi-mi:“MI:0915”(physical association)0.720
CEP57L1KATNAL1psi-mi:“MI:0915”(physical association)0.720
KATNAL1KLC4psi-mi:“MI:0915”(physical association)0.720
AIRIMKATNAL1psi-mi:“MI:0915”(physical association)0.720
KATNAL1COX17psi-mi:“MI:0915”(physical association)0.670
KATNAL1KATNAL1psi-mi:“MI:0915”(physical association)0.670
COX17KATNAL1psi-mi:“MI:0915”(physical association)0.670
PFDN1PFDN6psi-mi:“MI:0914”(association)0.640
KATNAL1CEP57L1psi-mi:“MI:0915”(physical association)0.560

BioGRID (50): KATNAL1 (Two-hybrid), KATNAL1 (Two-hybrid), KATNAL1 (Two-hybrid), KATNAL1 (Two-hybrid), KATNAL1 (Two-hybrid), KATNAL1 (Two-hybrid), KLC4 (Two-hybrid), CEP57L1 (Two-hybrid), KATNAL1 (Two-hybrid), KATNAL1 (Affinity Capture-MS), KATNAL1 (Synthetic Lethality), KATNAL1 (Two-hybrid), KATNAL1 (Two-hybrid), KATNAL1 (Two-hybrid), KATNAL1 (Two-hybrid)

ESM2 similar proteins: A0JMA9, A2VDN5, A8QFF6, A8XV40, A9RA82, B2RYN7, B3EX35, B3M301, B4QSF0, B4USW8, B5X3X5, B7NZ88, B7PXE3, F4IAE9, O14114, O15381, O16299, O59824, O75449, P34808, P54816, Q05AS3, Q0IIR9, Q1HGK7, Q3B8D5, Q4R407, Q5RDX4, Q5RII9, Q5U3S1, Q5XIK7, Q5ZK92, Q60QD1, Q6AZT2, Q6E0V2, Q6NW58, Q6P158, Q6PL18, Q719N1, Q8CDM1, Q8IYT4

Diamond homologs: A0JMA9, A2VDN5, A4IHT0, A8QFF6, A8XV40, A9RA82, B2RYN7, B3EX35, B3M301, B3P8A3, B4G437, B4HGG6, B4JII0, B4K799, B4M0H8, B4NBP4, B4PL32, B4QSF0, B4USW8, B5X3X5, B7NZ88, B7PXE3, D0FH76, D2VS83, F2Z6D2, F4JEX5, F6QV99, O05209, O16299, O28972, O43078, O61577, O75351, O75449, P25694, P34808, P39955, P40328, P46467, P52917

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance53
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2592 predictions. Top by Δscore:

VariantEffectΔscore
13:30208563:T:TAdonor_gain1.0000
13:30208575:A:ACdonor_gain1.0000
13:30208576:C:CCdonor_gain1.0000
13:30208576:CTT:Cdonor_gain1.0000
13:30208578:T:TAdonor_gain1.0000
13:30208607:G:Cdonor_gain1.0000
13:30208734:CATCC:Cacceptor_gain1.0000
13:30208736:TCC:Tacceptor_gain1.0000
13:30208737:CC:Cacceptor_gain1.0000
13:30208737:CCC:Cacceptor_gain1.0000
13:30208738:CC:Cacceptor_gain1.0000
13:30209162:C:CAdonor_gain1.0000
13:30227409:TACC:Tdonor_loss1.0000
13:30227411:C:CTdonor_loss1.0000
13:30227544:CTC:Cacceptor_gain1.0000
13:30227547:C:CCacceptor_gain1.0000
13:30227555:A:Tacceptor_gain1.0000
13:30231307:CACT:Cdonor_loss1.0000
13:30231308:ACTC:Adonor_loss1.0000
13:30231310:TCAC:Tdonor_loss1.0000
13:30231311:C:CGdonor_loss1.0000
13:30231312:A:ACdonor_gain1.0000
13:30231313:C:CCdonor_gain1.0000
13:30231313:CCAT:Cdonor_gain1.0000
13:30231468:ACACC:Aacceptor_gain1.0000
13:30231469:CACC:Cacceptor_gain1.0000
13:30231469:CACCC:Cacceptor_gain1.0000
13:30231470:ACC:Aacceptor_gain1.0000
13:30231471:CC:Cacceptor_gain1.0000
13:30231471:CCC:Cacceptor_gain1.0000

AlphaMissense

3230 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:30227447:C:AR371M1.000
13:30227447:C:GR371T1.000
13:30227482:A:CN359K1.000
13:30227482:A:TN359K1.000
13:30230482:A:GL333P1.000
13:30231414:G:TA262D1.000
13:30231420:G:TA260D1.000
13:30231421:C:GA260P1.000
13:30231426:G:TA258D1.000
13:30231441:C:TG253D1.000
13:30231447:C:TG251D1.000
13:30231448:C:GG251R1.000
13:30231456:C:TG248E1.000
13:30231457:C:GG248R1.000
13:30231457:C:TG248R1.000
13:30208714:T:AR433S0.999
13:30208714:T:GR433S0.999
13:30208715:C:AR433I0.999
13:30208715:C:GR433T0.999
13:30208733:G:TA427D0.999
13:30208734:C:GA427P0.999
13:30210318:G:CC424W0.999
13:30210319:C:TC424Y0.999
13:30210320:A:GC424R0.999
13:30210335:C:GD419H0.999
13:30210340:C:TG417D0.999
13:30210343:G:AS416F0.999
13:30210409:A:GL394P0.999
13:30210421:A:GL390P0.999
13:30210424:A:GL389P0.999

dbSNP variants (sampled 300 via entrez): RS1000004775 (13:30291555 T>A,C), RS1000048459 (13:30307105 C>G,T), RS1000068611 (13:30292060 C>T), RS1000101530 (13:30259123 A>G), RS1000123604 (13:30238841 A>C), RS1000144902 (13:30307252 G>A), RS1000148475 (13:30203698 T>C), RS1000176643 (13:30301490 A>G), RS1000226157 (13:30294495 T>C), RS1000289953 (13:30260080 CCTAACTGGGAGGTACCCCCCAGCAGG>C), RS1000307998 (13:30265911 C>CG), RS1000314931 (13:30260346 A>C,G), RS1000381371 (13:30266283 T>C,G), RS1000395723 (13:30285615 G>A,T), RS1000407452 (13:30241259 C>T)

Disease associations

OMIM: gene MIM:614764 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST001343_1Fat distribution (HIV)3.000000e-06
GCST001613_15Antineutrophil cytoplasmic antibody-associated vasculitis4.000000e-06
GCST003983_32Male-pattern baldness2.000000e-09
GCST004267_6Blood osmolality (transformed sodium)5.000000e-06
GCST008114_32Type 2 diabetes2.000000e-07
GCST010002_182Refractive error1.000000e-11
GCST011771_1Rapid response to perioperative phenylephrine (change in mean arterial pressure)2.000000e-08
GCST012490_501Femur bone mineral density x serum urate levels interaction3.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004341body fat distribution
EFO:0006943blood pressure change measurement
EFO:0004531urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression2
potassium chromate(VI)affects cotreatment, decreases expression2
Tretinoindecreases expression, increases expression2
triphenyl phosphateaffects expression1
lead acetateincreases expression1
testosterone undecanoateincreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
chromium hexavalent iondecreases expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
abrinedecreases expression1
Bortezomibincreases expression1
Resveratrolaffects cotreatment, increases expression1
Fulvestrantincreases methylation1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Cisplatinincreases expression1
Coumestrolaffects cotreatment, increases expression1
Drugs, Chinese Herbalincreases expression1
Estradiolaffects cotreatment, increases expression1
Lipopolysaccharidesaffects response to substance, increases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Naphthoquinonesincreases expression1
Quercetinincreases expression1
Rotenonedecreases expression1
Valproic Aciddecreases expression1

Clinical trials (associated diseases)

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