GeneBe

ATCAY

ATCAY kinesin light chain interacting caytaxin, the group of BCH domain containing

Basic information

Region (hg38): 19:3879864-3928082

Links

ENSG00000167654 ∙ NCBI:85300 ∙ OMIM:608179 ∙ HGNC:779 ∙ Uniprot:Q86WG3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Cayman type cerebellar ataxia (Supportive), mode of inheritance: AR
  • Cayman type cerebellar ataxia (Moderate), mode of inheritance: AR
  • Cayman type cerebellar ataxia (Strong), mode of inheritance: AR
  • cerebellar ataxia (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Ataxia, cerebellar, Cayman typeARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic14556008

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATCAY gene.

  • Inborn_genetic_diseases (56 variants)
  • Cayman_type_cerebellar_ataxia (40 variants)
  • not_provided (36 variants)
  • ATCAY-related_disorder (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATCAY gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033064.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
7
clinvar
17
clinvar
1
clinvar
 25
missense
1
clinvar
65
clinvar
1
clinvar
 67
nonsense
1
clinvar
 1
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total 2 0 73 18 1

Highest pathogenic variant AF is 6.8619016e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATCAYprotein_codingprotein_codingENST00000450849 1248216
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.6210.379124629061246350.0000241
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.611852580.7180.00001782451
Missense in Polyphen64110.220.580631023
Synonymous-0.4141161101.050.00000892692
Loss of Function3.38420.50.1958.77e-7234

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006470.0000646
Ashkenazi Jewish0.00009980.0000994
East Asian0.000.00
Finnish0.00009290.0000928
European (Non-Finnish)0.00001920.0000177
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
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. {ECO:0000269|PubMed:16899818}.;
Disease
DISEASE: 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. {ECO:0000269|PubMed:14556008}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Intolerance Scores

loftool
0.406
rvis_EVS
-0.54
rvis_percentile_EVS
20.54

Haploinsufficiency Scores

pHI
0.199
hipred
Y
hipred_score
0.774
ghis
0.604

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.152

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Atcay
Phenotype
endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype;

Zebrafish Information Network

Gene name
atcaya
Affected structure
motor neuron
Phenotype tag
abnormal
Phenotype quality
decreased length

Gene ontology

Biological process
polyphosphate catabolic process;apoptotic process;neuron projection development;regulation of protein localization;mitochondrion distribution;negative regulation of glutamate metabolic process
Cellular component
cytoplasm;mitochondrion;cell junction;axon;dendrite;mitochondrial membrane;neuron projection;synapse
Molecular function
exopolyphosphatase activity;protein binding;kinesin binding;WW domain binding