ATCAY

gene
On this page

Also known as BNIP-H

Summary

ATCAY (ATCAY kinesin light chain interacting caytaxin, HGNC:779) is a protein-coding gene on chromosome 19p13.3, encoding Caytaxin (Q86WG3). Functions in the development of neural tissues, particularly the postnatal maturation of the cerebellar cortex.

This gene encodes a neuron-restricted protein that contains a CRAL-TRIO motif common to proteins that bind small lipophilic molecules. Mutations in this gene are associated with cerebellar ataxia, Cayman type.

Source: NCBI Gene 85300 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Cayman type cerebellar ataxia (Strong, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 222 total — 4 pathogenic
  • Phenotypes (HPO): 23
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • MANE Select transcript: NM_033064

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:779
Approved symbolATCAY
NameATCAY kinesin light chain interacting caytaxin
Location19p13.3
Locus typegene with protein product
StatusApproved
AliasesBNIP-H
Ensembl geneENSG00000167654
Ensembl biotypeprotein_coding
OMIM608179
Entrez85300

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000450849, ENST00000595916, ENST00000597739, ENST00000598136, ENST00000600960, ENST00000601323, ENST00000861418

RefSeq mRNA: 1 — MANE Select: NM_033064 NM_033064

CCDS: CCDS45923

Canonical transcript exons

ENST00000450849 — 13 exons

ExonStartEnd
ENSE0000169772439245833928082
ENSE0000225827038806853881008
ENSE0000346536838857273885844
ENSE0000348375039207663920798
ENSE0000352199339094863909617
ENSE0000353556939077343907919
ENSE0000354938339177423917777
ENSE0000356385739024873902545
ENSE0000357417639082683908370
ENSE0000359584039188063918877
ENSE0000361005739137583913856
ENSE0000361511039108033910889
ENSE0000368946039054343905655

Expression profiles

Bgee: expression breadth ubiquitous, 150 present calls, max score 98.21.

FANTOM5 (CAGE): breadth broad, TPM avg 7.1659 / max 284.9070, expressed in 306 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1732427.1114305
1732440.054522

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277198.21gold quality
cortical plateUBERON:000534397.93gold quality
Brodmann (1909) area 23UBERON:001355497.67gold quality
superior frontal gyrusUBERON:000266197.36gold quality
endothelial cellCL:000011597.22gold quality
entorhinal cortexUBERON:000272897.12gold quality
ganglionic eminenceUBERON:000402396.94gold quality
postcentral gyrusUBERON:000258196.85gold quality
primary visual cortexUBERON:000243696.62gold quality
parietal lobeUBERON:000187296.47gold quality
Brodmann (1909) area 46UBERON:000648396.38gold quality
occipital lobeUBERON:000202195.46gold quality
dorsolateral prefrontal cortexUBERON:000983495.19gold quality
right frontal lobeUBERON:000281095.18gold quality
frontal cortexUBERON:000187095.13gold quality
neocortexUBERON:000195094.87gold quality
cerebral cortexUBERON:000095694.76gold quality
temporal lobeUBERON:000187194.54gold quality
Brodmann (1909) area 9UBERON:001354094.44gold quality
prefrontal cortexUBERON:000045194.27gold quality
anterior cingulate cortexUBERON:000983594.25gold quality
hypothalamusUBERON:000189893.71gold quality
amygdalaUBERON:000187692.87gold quality
Ammon’s hornUBERON:000195492.77gold quality
forebrainUBERON:000189092.61gold quality
cerebellar vermisUBERON:000472092.17gold quality
brainUBERON:000095592.12gold quality
lateral nuclear group of thalamusUBERON:000273691.94gold quality
superior vestibular nucleusUBERON:000722791.89gold quality
nucleus accumbensUBERON:000188291.58gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-84465yes27.89
E-GEOD-93593yes13.74
E-ANND-3yes3.89
E-GEOD-124858no12.41
E-MTAB-6678no3.40

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GLI3, NR2E1

miRNA regulators (miRDB)

112 targeting ATCAY, 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-4682100.0068.891258
HSA-MIR-4455100.0065.481587
HSA-MIR-574-5P100.0066.01989
HSA-MIR-4283100.0066.422097
HSA-MIR-4533100.0069.482758
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-150-5P99.9966.691976
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-426799.9666.532368
HSA-MIR-185-3P99.9567.011743
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-627-3P99.9071.423316
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-60999.8264.26505
HSA-MIR-489-3P99.8066.46839
HSA-MIR-129999.7771.242389
HSA-MIR-498-5P99.7669.641807
HSA-MIR-674599.7465.331321
HSA-MIR-1255A99.7468.09744
HSA-MIR-1255B-5P99.7468.16741
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-64699.6867.841645

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 4)

  • Using shotgun mass spectrometry, we found this protein differentially expressed in the dorsolateral prefrontal cortex from patients with schizophrenia. (PMID:19165527)
  • caytaxin binds to kinesin-1 and functions as an adaptor that mediates intracellular transport of specific cargos, one of which is the mitochondrion. (PMID:19861499)
  • Caytaxin’s role in maintaining normal neuronal function (PMID:23226316)
  • Novel homozygous variants in ATCAY, MCOLN1, and SACS in a complex movement disorder in five consanguineous Pakistani families. (PMID:29449188)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioatcaybENSDARG00000059781
danio_rerioatcayaENSDARG00000071678
mus_musculusAtcayENSMUSG00000034958
rattus_norvegicusAtcayENSRNOG00000020407
drosophila_melanogasterCG11593FBGN0035488

Paralogs (3): PRUNE2 (ENSG00000106772), BNIP2 (ENSG00000140299), BNIPL (ENSG00000163141)

Protein

Protein identifiers

CaytaxinQ86WG3 (reviewed: Q86WG3)

Alternative names: Ataxia cayman type protein, BNIP-2-homology

All UniProt accessions (4): Q86WG3, A0A0S2Z5T8, M0R197, M0R225

UniProt curated annotations — full annotation on UniProt →

Function. Functions in the development of neural tissues, particularly the postnatal maturation of the cerebellar cortex. May play a role in neurotransmission through regulation of glutaminase/GLS, an enzyme responsible for the production in neurons of the glutamate neurotransmitter. Alternatively, may regulate the localization of mitochondria within axons and dendrites.

Subunit / interactions. Interacts with KLC1; may link mitochondria to KLC1 and regulate mitochondria localization into neuron projections. Interacts with GLS; the interaction is direct and may control GLS localization, negatively regulating its activity. Interacts with PIN1 (via WW domain); upon NGF stimulation. The interaction with PIN1 and GLS is competitive. May interact with MAP2K2.

Subcellular location. Cell projection. Axon. Dendrite. Presynapse. Mitochondrion. Growth cone. Cytoplasm.

Post-translational modifications. Cleaved by CASP3 and CASP7. The potential C-terminal product released by CASP3 cleavage may inhibit the ERK signaling pathway through MAP2K2. May be ubiquitinated by STUB1.

Disease relevance. Cerebellar ataxia, cayman type (ATCAY) [MIM:601238] Found in a population isolate on Grand Cayman Island and causes a marked psychomotor retardation and prominent nonprogressive cerebellar dysfunction including nystagmus, intention tremor, dysarthria, and wide-based ataxic gait. Hypotonia is present from early childhood. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The CRAL-TRIO domain is known to bind small hydrophobic molecules.

Isoforms (2)

UniProt IDNamesCanonical?
Q86WG3-11yes
Q86WG3-32

RefSeq proteins (1): NP_149053* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001251CRAL-TRIO_domDomain
IPR022181Bcl2-/adenovirus-E1BFamily
IPR036865CRAL-TRIO_dom_sfHomologous_superfamily

Pfam: PF12496, PF13716

UniProt features (15 total): region of interest 4, mutagenesis site 3, compositionally biased region 2, chain 1, domain 1, sequence variant 1, sequence conflict 1, site 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86WG3-F170.680.40

Functional residue map

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

Catalytic / active sites (1): 105–106 (cleavage; by casp3)

Mutagenesis-validated functional residues (3):

PositionPhenotype
105alters cleavage by casp3.
115–117reduced interaction with klc1.
118–120completely abolishes interaction with klc1.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 138 (showing top): GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, GOBP_GLUTAMATE_METABOLIC_PROCESS, GOBP_NEUROGENESIS, GOBP_GLUTAMINE_FAMILY_AMINO_ACID_METABOLIC_PROCESS, FOXD3_01, GOBP_DICARBOXYLIC_ACID_METABOLIC_PROCESS, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOCC_NEURON_PROJECTION, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_MITOCHONDRION_LOCALIZATION, GOBP_ORGANELLE_LOCALIZATION, GOBP_MITOCHONDRION_DISTRIBUTION, GOBP_REGULATION_OF_AMINO_ACID_METABOLIC_PROCESS, GOCC_NEURON_PROJECTION_TERMINUS

GO Biological Process (6): apoptotic process (GO:0006915), neuron projection development (GO:0031175), regulation of protein localization (GO:0032880), mitochondrion distribution (GO:0048311), obsolete negative regulation of glutamate metabolic process (GO:2000212), nervous system development (GO:0007399)

GO Molecular Function (2): kinesin binding (GO:0019894), protein binding (GO:0005515)

GO Cellular Component (12): cytoplasm (GO:0005737), axon (GO:0030424), dendrite (GO:0030425), growth cone (GO:0030426), mitochondrial membrane (GO:0031966), neuron projection (GO:0043005), neuron projection terminus (GO:0044306), synapse (GO:0045202), perinuclear region of cytoplasm (GO:0048471), presynapse (GO:0098793), membrane (GO:0016020), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure6
neuron projection3
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
neuron development1
plasma membrane bounded cell projection organization1
intracellular protein localization1
regulation of localization1
mitochondrion localization1
system development1
cytoskeletal protein binding1
binding1
intracellular anatomical structure1
dendritic tree1
site of polarized growth1
distal axon1
mitochondrion1
mitochondrial envelope1
organelle membrane1
plasma membrane bounded cell projection1
cell junction1
cytoplasm1
synapse1

Protein interactions and networks

STRING

504 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ATCAYTTPAP49638912
ATCAYKLC1Q07866742
ATCAYFKBP1CQ5VVH2708
ATCAYGDAP1Q8TB36624
ATCAYSTUB1Q9UNE7512
ATCAYKLC2Q9H0B6447
ATCAYRAB6BQ9NRW1444
ATCAYC1orf94Q6P1W5435
ATCAYKLC4Q9NSK0375
ATCAYTOR1AO14656369
ATCAYKLC3Q6P597368
ATCAYCLSTN1O94985367
ATCAYAKAP13Q12802353
ATCAYCWF19L1Q69YN2321
ATCAYZFR2Q9UPR6311
ATCAYSPANXN2Q5MJ10311

IntAct

14 interactions, top by confidence:

ABTypeScore
ATCAYSTUB1psi-mi:“MI:0915”(physical association)0.630
STUB1ATCAYpsi-mi:“MI:0915”(physical association)0.630
KLC1ATCAYpsi-mi:“MI:0915”(physical association)0.560
ATCAYUBE2D2psi-mi:“MI:0220”(ubiquitination reaction)0.440
CDCA7CD33psi-mi:“MI:0914”(association)0.350
CNTFRCACNA2D1psi-mi:“MI:0914”(association)0.350
CXCR3RIMOC1psi-mi:“MI:0914”(association)0.350
POPDC2FZD6psi-mi:“MI:0914”(association)0.350
LPGAT1ATCAYpsi-mi:“MI:0914”(association)0.350
TARBP2H1-1psi-mi:“MI:0914”(association)0.350
KLC1ATCAYpsi-mi:“MI:0915”(physical association)0.000

BioGRID (13): ATCAY (Reconstituted Complex), STUB1 (Protein-peptide), ATCAY (Affinity Capture-Western), ATCAY (Reconstituted Complex), PIN1 (Reconstituted Complex), ATCAY (Affinity Capture-Western), GLS (Affinity Capture-Western), FATE1 (Two-hybrid), ATCAY (Two-hybrid), ATCAY (Affinity Capture-MS), STUB1 (Two-hybrid), ATCAY (Biochemical Activity), APP (Reconstituted Complex)

ESM2 similar proteins: A0JMA8, A1A535, A1A5P5, A3KMI0, A6H8H2, A8E7C5, E7F187, O15013, O54940, O88870, P41229, P41230, P43125, P70302, P84903, Q03606, Q0IHU9, Q12982, Q13586, Q1LYM3, Q1M168, Q38JA7, Q58CP9, Q5BJR4, Q5F259, Q5R4Q8, Q5R991, Q5RDF1, Q5U245, Q5VZ89, Q6DTM3, Q6H1V1, Q6P3S1, Q6ZPS6, Q6ZUJ8, Q7Z3E5, Q7Z401, Q803Q4, Q86WG3, Q86YR7

Diamond homologs: O54940, P85298, Q07960, Q0IHU9, Q12982, Q1M168, Q52KR3, Q54TH9, Q55AR6, Q5BJR4, Q5FWK3, Q5R4Q8, Q7Z465, Q86WG3, Q8BHE3, Q8WUY3, Q99JU7, Q9CXP4, Q9GKT0, Q9VTU3, A4IF90, A6NI28, A7T167, B2RQE8, B2RTY4, B2RWW0, B9VTT2, D3ZFJ3, D3ZZN9, E7EZG2, E7F3F0, F1LQX4, O14014, O43182, O54834, O94988, P34288, P35688, P42331, P55194

SIGNOR signaling

1 interactions.

AEffectBMechanism
STUB1“down-regulates quantity by destabilization”ATCAYpolyubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic0
Uncertain significance146
Likely benign27
Benign30

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
1319958NM_033064.5(ATCAY):c.602_608del (p.Asp201fs)Pathogenic
1338347NM_033064.5(ATCAY):c.903C>G (p.Ser301Arg)Pathogenic
1338348NM_033064.5(ATCAY):c.965+3G>TPathogenic
4293711NM_033064.5(ATCAY):c.556G>T (p.Glu186Ter)Pathogenic

SpliceAI

1887 predictions. Top by Δscore:

VariantEffectΔscore
19:3885722:TTCA:Tacceptor_loss1.0000
19:3885724:CAGGG:Cacceptor_loss1.0000
19:3885725:A:ACacceptor_loss1.0000
19:3885725:A:AGacceptor_gain1.0000
19:3885725:AG:Aacceptor_gain1.0000
19:3885725:AGG:Aacceptor_gain1.0000
19:3885726:G:GGacceptor_gain1.0000
19:3885726:GG:Gacceptor_gain1.0000
19:3885726:GGG:Gacceptor_gain1.0000
19:3885726:GGGGT:Gacceptor_gain1.0000
19:3885842:CAG:Cdonor_loss1.0000
19:3885843:AGGTA:Adonor_loss1.0000
19:3885845:G:Adonor_loss1.0000
19:3885846:T:Gdonor_loss1.0000
19:3902386:T:TAacceptor_gain1.0000
19:3902390:T:TAacceptor_gain1.0000
19:3905423:T:Gacceptor_gain1.0000
19:3905429:TGCA:Tacceptor_loss1.0000
19:3905430:GCAG:Gacceptor_loss1.0000
19:3905431:CA:Cacceptor_loss1.0000
19:3905432:A:ACacceptor_loss1.0000
19:3905432:A:AGacceptor_gain1.0000
19:3905433:G:GCacceptor_gain1.0000
19:3905433:GC:Gacceptor_gain1.0000
19:3905433:GCT:Gacceptor_gain1.0000
19:3905433:GCTC:Gacceptor_gain1.0000
19:3905433:GCTCC:Gacceptor_gain1.0000
19:3905652:G:GTdonor_gain1.0000
19:3905652:GAAG:Gdonor_gain1.0000
19:3905653:A:Tdonor_gain1.0000

AlphaMissense

2464 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:3907908:T:AV178D1.000
19:3907917:G:AG181E1.000
19:3908268:G:AG182E1.000
19:3908319:T:CL199P1.000
19:3908322:C:AP200Q1.000
19:3908364:T:CL214P1.000
19:3909526:T:CY230H1.000
19:3909583:T:AW249R1.000
19:3909583:T:CW249R1.000
19:3909585:G:CW249C1.000
19:3909585:G:TW249C1.000
19:3909587:T:CL250P1.000
19:3909598:T:GY254D1.000
19:3910805:T:CL261S1.000
19:3910810:A:GK263E1.000
19:3910811:A:CK263T1.000
19:3910811:A:TK263I1.000
19:3910812:A:CK263N1.000
19:3910812:A:TK263N1.000
19:3910817:T:AL265Q1.000
19:3910817:T:CL265P1.000
19:3910832:T:AI270N1.000
19:3910835:T:AV271D1.000
19:3913765:T:CF292L1.000
19:3913766:T:CF292S1.000
19:3913766:T:GF292C1.000
19:3913767:C:AF292L1.000
19:3913767:C:GF292L1.000
19:3913774:A:GK295E1.000
19:3913776:G:CK295N1.000

dbSNP variants (sampled 300 via entrez): RS1000017248 (19:3890324 G>A), RS1000150164 (19:3886161 C>A), RS1000226971 (19:3918167 G>A,T), RS1000248597 (19:3916050 C>G,T), RS1000284091 (19:3905307 T>C), RS1000332041 (19:3911057 G>T), RS1000349615 (19:3915183 A>T), RS1000384166 (19:3886406 C>T), RS1000434753 (19:3887268 G>A), RS1000436834 (19:3915464 C>T), RS1000502926 (19:3911804 A>C,G), RS1000640226 (19:3912055 A>G), RS1000674924 (19:3912198 C>A,G,T), RS1000688352 (19:3905967 T>C), RS1000706266 (19:3911911 C>A,T)

Disease associations

OMIM: gene MIM:608179 | disease phenotypes: MIM:601238

GenCC curated gene-disease

DiseaseClassificationInheritance
Cayman type cerebellar ataxiaStrongAutosomal recessive

Mondo (1): Cayman type cerebellar ataxia (MONDO:0011025)

Orphanet (1): Cerebellar ataxia, Cayman type (Orphanet:94122)

HPO phenotypes

23 total (23 of 23 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000338Hypomimic face
HP:0000479Abnormal retinal morphology
HP:0000486Strabismus
HP:0000639Nystagmus
HP:0001251Ataxia
HP:0001252Hypotonia
HP:0001260Dysarthria
HP:0001263Global developmental delay
HP:0001272Cerebellar atrophy
HP:0001290Generalized hypotonia
HP:0001321Cerebellar hypoplasia
HP:0001332Dystonia
HP:0001763Pes planus
HP:0002066Gait ataxia
HP:0002067Bradykinesia
HP:0002078Truncal ataxia
HP:0002080Intention tremor
HP:0002136Broad-based gait
HP:0002470Nonprogressive cerebellar ataxia
HP:0003202Skeletal muscle atrophy
HP:0003577Congenital onset
HP:0003593Infantile onset

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001166_1Aging (time to event)3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0022597aging

MeSH disease descriptors (1)

DescriptorNameTree numbers
C563363Cerebellar Ataxia, Cayman Type (supp.)

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
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, decreases expression2
Benzo(a)pyreneaffects methylation, decreases methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Valproic Acidaffects expression, increases expression2
Cadmium Chlorideincreases abundance, increases expression2
propionaldehydeincreases expression1
bisphenol Aaffects cotreatment, decreases methylation1
butyraldehydeincreases expression1
benzo(e)pyreneincreases methylation1
pentanalincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
licochalcone Bincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Vorinostatdecreases expression1
Aldehydesincreases expression1
Cadmiumincreases abundance, increases expression1
Carbamazepineaffects expression1
Diethylhexyl Phthalatedecreases expression1
Lipopolysaccharidesaffects response to substance, increases expression, decreases expression1
Methapyrileneincreases methylation1
Niclosamideincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Tretinoindecreases expression1
Aflatoxin B1increases methylation1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford