KNCN

Summary

KNCN (kinocilin, HGNC:26488) is a protein-coding gene on chromosome 1p33, encoding Kinocilin (A6PVL3). May play a role in stabilizing dense microtubular networks or in vesicular trafficking.

Predicted to be located in several cellular components, including apical part of cell; cytoplasm; and microtubule cytoskeleton. Predicted to be active in several cellular components, including apical plasma membrane; cytoskeleton; and kinocilium.

Source: NCBI Gene 148930 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_001322255

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26488
Approved symbol	KNCN
Name	kinocilin
Location	1p33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32011, KINO, L5
Ensembl gene	ENSG00000162456
Ensembl biotype	protein_coding
OMIM	611455
Entrez	148930

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000294445, ENST00000396314, ENST00000481882, ENST00000524908

RefSeq mRNA: 2 — MANE Select: NM_001322255 NM_001097611, NM_001322255

CCDS: CCDS44133, CCDS81316

Canonical transcript exons

ENST00000481882 — 4 exons

Exon	Start	End
ENSE00001065374	46545641	46547809
ENSE00001524555	46549934	46550002
ENSE00001923073	46551065	46551647
ENSE00003506669	46549193	46549267

Expression profiles

Bgee: expression breadth broad, 53 present calls, max score 71.28.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0108 / max 5.4130, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12183	0.0108	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	71.28	gold quality
prefrontal cortex	UBERON:0000451	66.65	gold quality
nucleus accumbens	UBERON:0001882	64.96	gold quality
right uterine tube	UBERON:0001302	63.64	gold quality
hypothalamus	UBERON:0001898	63.40	gold quality
amygdala	UBERON:0001876	59.51	gold quality
caudate nucleus	UBERON:0001873	59.42	gold quality
frontal cortex	UBERON:0001870	58.97	gold quality
putamen	UBERON:0001874	58.46	gold quality
mucosa of paranasal sinus	UBERON:0005030	58.06	gold quality
neocortex	UBERON:0001950	57.91	gold quality
Brodmann (1909) area 9	UBERON:0013540	57.88	gold quality
right frontal lobe	UBERON:0002810	57.47	gold quality
anterior cingulate cortex	UBERON:0009835	56.76	gold quality
trabecular bone tissue	UBERON:0002483	55.84	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	55.64	gold quality
forebrain	UBERON:0001890	55.58	gold quality
cerebral cortex	UBERON:0000956	55.10	gold quality
vena cava	UBERON:0004087	54.41	gold quality
left testis	UBERON:0004533	53.48	gold quality
esophagus squamous epithelium	UBERON:0006920	52.63	gold quality
temporal lobe	UBERON:0001871	52.58	gold quality
primary visual cortex	UBERON:0002436	52.46	gold quality
Brodmann (1909) area 23	UBERON:0013554	52.30	gold quality
cortical plate	UBERON:0005343	52.29	gold quality
testis	UBERON:0000473	52.27	gold quality
Ammon’s horn	UBERON:0001954	51.91	gold quality
cartilage tissue	UBERON:0002418	51.90	gold quality
brain	UBERON:0000955	51.38	gold quality
substantia nigra	UBERON:0002038	51.25	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Kncn	ENSMUSG00000073774
rattus_norvegicus	Kncn	ENSRNOG00000089117

Protein

Protein identifiers

Kinocilin — A6PVL3 (reviewed: A6PVL3)

All UniProt accessions (1): A6PVL3

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in stabilizing dense microtubular networks or in vesicular trafficking.

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
A6PVL3-1	1	yes
A6PVL3-2	2

RefSeq proteins (2): NP_001091080, NP_001309184* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027837	Kinocilin	Family

Pfam: PF15033

UniProt features (7 total): transmembrane region 2, compositionally biased region 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6PVL3-F1	60.15	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): GCANCTGNY_MYOD_Q6, CAGCTG_AP4_Q5, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOCC_APICAL_PLASMA_MEMBRANE, GOCC_NEURON_PROJECTION, GOCC_APICAL_PART_OF_CELL, GOCC_STEREOCILIUM_BUNDLE, GOCC_CLUSTER_OF_ACTIN_BASED_CELL_PROJECTIONS, GOCC_PLASMA_MEMBRANE_REGION, GOCC_CELL_BODY, GOCC_SOMATODENDRITIC_COMPARTMENT, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY, SCGGAAGY_ELK1_02, HEB_Q6

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (9): apical plasma membrane (GO:0016324), cuticular plate (GO:0032437), ciliary basal body (GO:0036064), neuronal cell body (GO:0043025), kinocilium (GO:0060091), cytoplasm (GO:0005737), microtubule cytoskeleton (GO:0015630), membrane (GO:0016020), apical part of cell (GO:0045177)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
apical part of cell	1
plasma membrane region	1
cortical actin cytoskeleton	1
microtubule organizing center	1
cilium	1
somatodendritic compartment	1
cell body	1
radial spoke	1
stereocilium bundle	1
neuron projection	1
organelle	1
9+2 non-motile cilium	1
intracellular anatomical structure	1
cytoskeleton	1

Protein interactions and networks

STRING

276 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KNCN	MKNK1	Q9BUB5	805
KNCN	KLHL23	Q8NBE8	485
KNCN	C3orf62	Q6ZUJ4	477
KNCN	CDHR4	A6H8M9	432
KNCN	GORAB	Q5T7V8	401
KNCN	DNAJC5B	Q9UF47	399
KNCN	ZNF649	Q9BS31	392
KNCN	CYFIP2	Q96F07	378
KNCN	CHRNA10	Q9GZZ6	376
KNCN	A0A096LNH4	A0A096LNH4	371
KNCN	SYT15	Q9BQS2	369
KNCN	CYFIP1	Q7L576	367
KNCN	CYTH4	Q9UIA0	359
KNCN	ZSCAN31	Q96LW9	357
KNCN	ZKSCAN2	Q63HK3	351

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A087WTH1, A0A125YWU9, A0PK84, A6PVL3, C9JQL5, F1QHM7, F1QX91, O15503, O41933, O70418, O88728, P0DI73, P13164, P26376, Q01628, Q01629, Q08755, Q0II74, Q21642, Q32L65, Q3UNB8, Q3YBM2, Q5FVR1, Q5FWL7, Q5I0I2, Q5R8D6, Q5RF75, Q5Y5T3, Q6DHI1, Q76IC6, Q7M734, Q7TQJ1, Q8BGI3, Q8CES1, Q8CFA6, Q8IYP9, Q8N6L7, Q8WVZ1, Q91WU6, Q921C1

Diamond homologs: A6PVL3, Q307W7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

654 predictions. Top by Δscore:

Variant	Effect	Δscore
1:46550003:C:CC	acceptor_gain	1.0000
1:46551060:CTCA:C	donor_loss	1.0000
1:46551061:TCA:T	donor_loss	1.0000
1:46551062:CACCC:C	donor_loss	1.0000
1:46551063:A:AC	donor_gain	1.0000
1:46551063:AC:A	donor_gain	1.0000
1:46551063:ACCC:A	donor_loss	1.0000
1:46551064:C:A	donor_loss	1.0000
1:46551064:C:CC	donor_gain	1.0000
1:46551064:CC:C	donor_gain	1.0000
1:46549704:T:TA	donor_gain	0.9900
1:46549705:C:A	donor_gain	0.9900
1:46549928:CCTCA:C	donor_loss	0.9900
1:46549929:CTCA:C	donor_loss	0.9900
1:46549930:TCAC:T	donor_loss	0.9900
1:46549931:CAC:C	donor_loss	0.9900
1:46549932:ACCT:A	donor_loss	0.9900
1:46550000:GCC:G	acceptor_gain	0.9900
1:46550000:GCCCT:G	acceptor_loss	0.9900
1:46550001:CC:C	acceptor_gain	0.9900
1:46550001:CCC:C	acceptor_gain	0.9900
1:46550002:CC:C	acceptor_gain	0.9900
1:46550003:C:A	acceptor_loss	0.9900
1:46550004:T:A	acceptor_loss	0.9900
1:46551059:GCTCA:G	donor_loss	0.9900
1:46551063:ACC:A	donor_gain	0.9900
1:46551064:CCC:C	donor_gain	0.9900
1:46549998:GAGCC:G	acceptor_gain	0.9800
1:46551064:CCCAG:C	donor_gain	0.9800
1:46549932:A:AC	donor_gain	0.9700

AlphaMissense

797 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:46551138:G:C	S26R	0.982
1:46551138:G:T	S26R	0.982
1:46551140:T:G	S26R	0.982
1:46551079:C:T	G46D	0.930
1:46551065:C:G	G51R	0.929
1:46551065:C:T	G51R	0.929
1:46551080:C:G	G46R	0.929
1:46551143:C:G	G25R	0.926
1:46551155:C:G	G21R	0.924
1:46551155:C:T	G21R	0.924
1:46551084:A:C	F44L	0.921
1:46551084:A:T	F44L	0.921
1:46551086:A:G	F44L	0.921
1:46551142:C:T	G25D	0.921
1:46551145:G:T	A24D	0.918
1:46551095:C:G	G41R	0.910
1:46551094:C:T	G41D	0.875
1:46551154:C:T	G21E	0.874
1:46551128:C:G	G30R	0.871
1:46551127:C:T	G30D	0.869
1:46551073:G:T	A48D	0.867
1:46551167:A:G	C17R	0.867
1:46550002:C:T	G51E	0.860
1:46551092:C:G	G42R	0.851
1:46551091:C:T	G42D	0.845
1:46551151:A:C	L22R	0.841
1:46551076:G:T	A47D	0.840
1:46551160:G:T	A19D	0.818
1:46551085:A:G	F44S	0.803
1:46551065:C:A	G51W	0.793

dbSNP variants (sampled 300 via entrez): RS1000034743 (1:46549538 T>C), RS1000088476 (1:46549792 A>G,T), RS1000698256 (1:46545537 GA>G), RS1000802485 (1:46546212 C>G,T), RS1000920302 (1:46546481 A>G), RS1001091566 (1:46548543 C>T), RS1001304309 (1:46545811 C>T), RS1002242310 (1:46547127 C>T), RS1002465332 (1:46546899 G>T), RS1002981230 (1:46546718 C>T), RS1003095336 (1:46546491 C>T), RS1003135537 (1:46549000 G>A), RS1003249848 (1:46548063 G>C), RS1003327587 (1:46549234 T>G), RS1003877013 (1:46547842 C>A,T)

Disease associations

OMIM: gene MIM:611455 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003996_24	Monobrow	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007906	synophrys measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-palmitoylglycerol	increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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