KATNBL1

Summary

KATNBL1 (katanin regulatory subunit B1 like 1, HGNC:26199) is a protein-coding gene on chromosome 15q14, encoding KATNB1-like protein 1 (Q9H079). Regulates microtubule-severing activity of KATNAL1 in a concentration-dependent manner in vitro.

Predicted to enable microtubule binding activity. Involved in cytoplasmic microtubule organization and positive regulation of cytoskeleton organization. Located in several cellular components, including cleavage furrow; mitotic spindle pole; and nuclear lumen. Part of katanin complex.

Source: NCBI Gene 79768 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 65 total — 2 pathogenic
• MANE Select transcript: NM_024713

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26199
Approved symbol	KATNBL1
Name	katanin regulatory subunit B1 like 1
Location	15q14
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22557
Ensembl gene	ENSG00000134152
Ensembl biotype	protein_coding
OMIM	616235
Entrez	79768

Gene structure

Transcript identifiers

Ensembl transcripts: 45 — 38 protein_coding, 6 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000256544, ENST00000540594, ENST00000557877, ENST00000558473, ENST00000558681, ENST00000559462, ENST00000559464, ENST00000559515, ENST00000559760, ENST00000560108, ENST00000560247, ENST00000560308, ENST00000560310, ENST00000560671, ENST00000560915, ENST00000561270, ENST00000561371, ENST00000868187, ENST00000868188, ENST00000868189, ENST00000868190, ENST00000868191, ENST00000868192, ENST00000868193, ENST00000868194, ENST00000868195, ENST00000868196, ENST00000868197, ENST00000868198, ENST00000868199, ENST00000868200, ENST00000868201, ENST00000868202, ENST00000868203, ENST00000868204, ENST00000913325, ENST00000913326, ENST00000913327, ENST00000913328, ENST00000913329, ENST00000913330, ENST00000955235, ENST00000955236, ENST00000955237, ENST00000955238

RefSeq mRNA: 1 — MANE Select: NM_024713 NM_024713

CCDS: CCDS10034

Canonical transcript exons

ENST00000256544 — 10 exons

Exon	Start	End
ENSE00000881113	34145398	34145491
ENSE00000912966	34146761	34146850
ENSE00000912968	34147200	34147289
ENSE00001043279	34140674	34142371
ENSE00002209731	34209951	34210096
ENSE00003487634	34148632	34148750
ENSE00003602032	34154644	34154684
ENSE00003622699	34147380	34147430
ENSE00003686010	34152790	34153069
ENSE00003793181	34163560	34163690

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 98.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2210 / max 254.1405, expressed in 1734 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
149229	3.4372	1478
149230	3.4098	1521
149224	1.1474	124
149228	0.2266	97

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	98.10	gold quality
esophagus mucosa	UBERON:0002469	95.42	gold quality
vagina	UBERON:0000996	94.79	gold quality
nerve	UBERON:0001021	94.45	gold quality
tibial nerve	UBERON:0001323	94.45	gold quality
buccal mucosa cell	CL:0002336	94.41	gold quality
amniotic fluid	UBERON:0000173	94.24	gold quality
oral cavity	UBERON:0000167	94.23	gold quality
esophagus	UBERON:0001043	93.86	gold quality
adrenal tissue	UBERON:0018303	93.77	gold quality
sperm	CL:0000019	93.67	gold quality
esophagus squamous epithelium	UBERON:0006920	93.67	gold quality
ectocervix	UBERON:0012249	93.47	gold quality
rectum	UBERON:0001052	93.46	gold quality
body of uterus	UBERON:0009853	93.30	gold quality
skin of abdomen	UBERON:0001416	93.29	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.13	gold quality
cerebellar hemisphere	UBERON:0002245	93.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.06	gold quality
cerebellar cortex	UBERON:0002129	92.98	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.95	gold quality
right lung	UBERON:0002167	92.87	gold quality
ventricular zone	UBERON:0003053	92.87	gold quality
sural nerve	UBERON:0015488	92.70	gold quality
left uterine tube	UBERON:0001303	92.27	gold quality
omental fat pad	UBERON:0010414	92.16	gold quality
peritoneum	UBERON:0002358	92.14	gold quality
ascending aorta	UBERON:0001496	92.07	gold quality
lower esophagus	UBERON:0013473	92.07	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

204 targeting KATNBL1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790

Literature-anchored findings (GeneRIF, showing 1)

• Data indicate that KATNBL1 functions as a regulator of Katanin A subunit microtubule-severing activity during mitosis and that it likely coordinates with KATNB1 to perform this function. (PMID:26929214)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	katnbl1	ENSDARG00000042522
mus_musculus	Katnbl1	ENSMUSG00000027132
rattus_norvegicus	Katnbl1	ENSRNOG00000005814

Protein

Protein identifiers

KATNB1-like protein 1 — Q9H079 (reviewed: Q9H079)

Alternative names: Katanin p80 subunit B-like 1

All UniProt accessions (10): Q9H079, H0YKW3, H0YL62, H0YLP4, H0YLX9, H0YMR8, H0YNF7, H0YNG2, H0YNH1, H0YNW3

UniProt curated annotations — full annotation on UniProt →

Function. Regulates microtubule-severing activity of KATNAL1 in a concentration-dependent manner in vitro.

Subunit / interactions. Interacts with KATNA1 and KATNAL1; these interactions are competed by KATNB1 which has a higher affinity for them.

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

RefSeq proteins (1): NP_078989* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028021	Katanin_C-terminal	Domain
IPR042404	KATNBL1	Family

Pfam: PF13925

UniProt features (14 total): mutagenesis site 10, short sequence motif 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H079-F1	70.24	0.45

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): 61

Mutagenesis-validated functional residues (10):

Position	Phenotype
71	redistributes from the nucleus to both nucleus and cytoplasm; when associated with a-72; a-73 and a-74. complete redistr
72	redistributes from the nucleus to both nucleus and cytoplasm; when associated with a-71; a-73 and a-74. complete redistr
73	redistributes from the nucleus to both nucleus and cytoplasm; when associated with a-71; a-72 and a-74. complete redistr
74	redistributes from the nucleus to both nucleus and cytoplasm; when associated with a-71; a-72 and a-73. complete redistr
9	complete redistribution from the nucleus to the cytoplasm; when associated with a-10; a-11; a-26; a-27; a-28; a-71; a-72
10	complete redistribution from the nucleus to the cytoplasm; when associated with a-9; a-11; a-26; a-27; a-28; a-71; a-72;
11	complete redistribution from the nucleus to the cytoplasm; when associated with a-9; a-10; a-26; a-27; a-28; a-71; a-72;
26	complete redistribution from the nucleus to the cytoplasm; when associated with a-9; a-10; a-11; a-27; a-28; a-71; a-72;
27	complete redistribution from the nucleus to the cytoplasm; when associated with a-9; a-10; a-11; a-26; a-28; a-71; a-72;
28	complete redistribution from the nucleus to the cytoplasm; when associated with a-9; a-10; a-11; a-26; a-27; a-71; a-72;

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 215 (showing top): ACTACCT_MIR196A_MIR196B, GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, chr15q14, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOCC_MICROTUBULE_ORGANIZING_CENTER, AAACCAC_MIR140, WANG_LMO4_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, BENPORATH_NOS_TARGETS, AACTGGA_MIR145, GOBP_REGULATION_OF_CYTOSKELETON_ORGANIZATION, MILI_PSEUDOPODIA_CHEMOTAXIS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOCC_SPINDLE

GO Biological Process (2): cytoplasmic microtubule organization (GO:0031122), positive regulation of cytoskeleton organization (GO:0051495)

GO Molecular Function (2): microtubule binding (GO:0008017), protein binding (GO:0005515)

GO Cellular Component (12): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), katanin complex (GO:0008352), microtubule cytoskeleton (GO:0015630), midbody (GO:0030496), cleavage furrow (GO:0032154), mitotic spindle (GO:0072686), mitotic spindle pole (GO:0097431), spindle pole (GO:0000922), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
nuclear lumen	2
intracellular membraneless organelle	2
spindle	2
microtubule cytoskeleton organization	1
supramolecular fiber organization	1
cytoskeleton organization	1
positive regulation of organelle organization	1
regulation of cytoskeleton organization	1
tubulin binding	1
binding	1
intracellular membrane-bounded organelle	1
microtubule organizing center	1
microtubule associated complex	1
cytoskeleton	1
cell division site	1
plasma membrane region	1
spindle pole	1
mitotic spindle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

384 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KATNBL1	KATNA1	O75449	744
KATNBL1	KATNAL2	Q8IYT4	625
KATNBL1	KATNB1	Q9BVA0	577
KATNBL1	KATNAL1	Q9BW62	577
KATNBL1	MIX23	Q4VC31	572
KATNBL1	ZZEF1	O43149	532
KATNBL1	ZNF805	Q5CZA5	509
KATNBL1	NCAPD3	P42695	487
KATNBL1	TIMM21	Q9BVV7	480
KATNBL1	ANO5	Q75V66	455
KATNBL1	OR2F1	Q13607	445
KATNBL1	IFT172	Q9UG01	426
KATNBL1	FAM221A	A4D161	418
KATNBL1	FAM219B	Q5XKK7	398
KATNBL1	PRR9	Q5T870	383

IntAct

165 interactions, top by confidence:

A	B	Type	Score
KATNAL1	KATNBL1	psi-mi:“MI:0915”(physical association)	0.880
KATNBL1	KATNAL1	psi-mi:“MI:0915”(physical association)	0.880
MFAP1	KATNBL1	psi-mi:“MI:0915”(physical association)	0.780
KATNBL1	MFAP1	psi-mi:“MI:0915”(physical association)	0.780
KATNBL1	KATNA1	psi-mi:“MI:0915”(physical association)	0.770
KATNA1	KATNB1	psi-mi:“MI:0915”(physical association)	0.770
KATNBL1	KATNA1	psi-mi:“MI:0914”(association)	0.770
KATNA1	KATNB1	psi-mi:“MI:0914”(association)	0.770
PIBF1	KATNBL1	psi-mi:“MI:0915”(physical association)	0.560
CPNE2	KATNBL1	psi-mi:“MI:0915”(physical association)	0.560
KATNBL1	NXF1	psi-mi:“MI:0915”(physical association)	0.560
NTAQ1	KATNBL1	psi-mi:“MI:0915”(physical association)	0.560
CLIC3	KATNBL1	psi-mi:“MI:0915”(physical association)	0.560
PRKAB2	KATNBL1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (59): KATNBL1 (Two-hybrid), KATNBL1 (Two-hybrid), KATNAL1 (Two-hybrid), KATNA1 (Affinity Capture-MS), KATNB1 (Affinity Capture-MS), KATNBL1 (Affinity Capture-MS), KATNBL1 (Affinity Capture-MS), KATNBL1 (Affinity Capture-MS), KATNA1 (Affinity Capture-MS), KATNB1 (Affinity Capture-MS), KATNBL1 (Two-hybrid), KAT7 (Two-hybrid), KATNBL1 (Two-hybrid), KATNBL1 (Two-hybrid), HAP1 (Two-hybrid)

ESM2 similar proteins: A2RRS8, A4D1B5, A5PLK6, D3Z6S9, E7FA21, G3UYX5, O75747, O75901, O88480, O88869, Q2T9P0, Q3UMB5, Q3UPC7, Q3URV1, Q402B2, Q4R9E9, Q5SUS0, Q5T0N1, Q5XI56, Q5XX13, Q642P2, Q6DHV5, Q6INI0, Q6P2C0, Q7L0X2, Q80X60, Q86VV8, Q86WZ0, Q8CDN1, Q8IV33, Q8IXR9, Q8K342, Q8N7B9, Q8N7X0, Q8ND61, Q8NE09, Q8NG48, Q8R4Y8, Q8TDY2, Q8TEV9

Diamond homologs: A0A1P8AW69, F4HTH8, F4KB17, O61585, Q13685, Q3SZK1, Q4V7Y7, Q5RAC9, Q5RCG7, Q5ZIU8, Q676U5, Q6NVM2, Q7YR70, Q7ZUV2, Q8BG40, Q8H0T9, Q9BVA0, Q9H079, Q9CWJ3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	45
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1712253	GRCh37/hg19 15q13.3-14(chr15:32915722-34671601)x3	Pathogenic
57876	GRCh38/hg38 15q13.3-14(chr15:32326136-39394068)x1	Pathogenic

SpliceAI

2390 predictions. Top by Δscore:

Variant	Effect	Δscore
15:34145055:ATC:A	donor_gain	1.0000
15:34145402:G:C	donor_gain	1.0000
15:34145487:TATTT:T	acceptor_gain	1.0000
15:34145489:TTT:T	acceptor_gain	1.0000
15:34145490:TT:T	acceptor_gain	1.0000
15:34145491:TCTAA:T	acceptor_loss	1.0000
15:34145492:C:CC	acceptor_gain	1.0000
15:34145492:C:T	acceptor_loss	1.0000
15:34145493:T:A	acceptor_loss	1.0000
15:34147198:A:AC	donor_gain	1.0000
15:34147199:C:CC	donor_gain	1.0000
15:34147199:CT:C	donor_gain	1.0000
15:34148627:CTTA:C	donor_loss	1.0000
15:34148628:TTAC:T	donor_loss	1.0000
15:34148629:TA:T	donor_loss	1.0000
15:34148630:A:C	donor_loss	1.0000
15:34152785:CTTA:C	donor_loss	1.0000
15:34152786:TTA:T	donor_loss	1.0000
15:34152787:TA:T	donor_loss	1.0000
15:34152788:A:T	donor_loss	1.0000
15:34152789:C:CA	donor_loss	1.0000
15:34152789:CCT:C	donor_gain	1.0000
15:34163553:GACTT:G	donor_loss	1.0000
15:34163554:ACTTA:A	donor_loss	1.0000
15:34163555:CTTA:C	donor_loss	1.0000
15:34163556:TTACC:T	donor_loss	1.0000
15:34163557:TACC:T	donor_loss	1.0000
15:34163558:A:AC	donor_gain	1.0000
15:34163558:A:C	donor_loss	1.0000
15:34163558:ACCT:A	donor_gain	1.0000

AlphaMissense

2008 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:34146828:A:G	W241R	0.994
15:34146828:A:T	W241R	0.994
15:34145402:G:T	A293D	0.990
15:34148686:G:T	A168D	0.990
15:34148706:C:A	R161S	0.989
15:34148706:C:G	R161S	0.989
15:34146819:C:G	A244P	0.988
15:34148707:C:A	R161M	0.988
15:34147398:A:G	L197P	0.987
15:34147402:A:G	C196R	0.987
15:34148707:C:G	R161T	0.986
15:34146836:C:T	G238D	0.984
15:34145403:C:G	A293P	0.983
15:34147398:A:C	L197R	0.983
15:34146837:C:G	G238R	0.982
15:34147252:A:G	C216R	0.980
15:34147398:A:T	L197H	0.979
15:34148650:A:G	L180P	0.979
15:34146824:A:G	L242P	0.978
15:34147205:A:C	F231L	0.978
15:34147205:A:T	F231L	0.978
15:34147207:A:G	F231L	0.978
15:34145411:C:T	G290D	0.976
15:34146815:A:T	V245D	0.976
15:34148695:A:G	L165S	0.975
15:34145465:A:G	L272S	0.974
15:34147423:C:G	D189H	0.974
15:34148687:C:G	A168P	0.972
15:34147218:A:G	L227P	0.970
15:34148716:A:G	L158S	0.969

dbSNP variants (sampled 300 via entrez): RS1000025606 (15:34175016 G>A,C), RS1000191873 (15:34174250 T>A), RS1000214120 (15:34158811 T>A,C), RS1000247135 (15:34197261 C>T), RS1000274097 (15:34159021 G>A), RS1000341315 (15:34146612 G>C), RS1000355751 (15:34206538 T>A), RS1000375818 (15:34191562 TAGA>T), RS1000390870 (15:34180193 T>G), RS1000396461 (15:34206224 C>T), RS1000445735 (15:34153259 A>T), RS1000452318 (15:34192130 C>T), RS1000480830 (15:34208256 T>C), RS1000518315 (15:34147628 G>A,C,T), RS1000538937 (15:34163787 A>G)

Disease associations

OMIM: gene MIM:616235 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases expression	4
mercuric bromide	increases expression, affects cotreatment	2
Acetaminophen	affects expression, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Cadmium Chloride	increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	decreases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, increases reaction	1
methylparaben	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
NSC 689534	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Aldehydes	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Plant Extracts	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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