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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ataxia, cerebellar, Cayman type	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	14556008

ClinVar

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

• not provided (2 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			6	9	1	16
missense	1		51			52
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region	1		3	4	1	9
non coding			72	14	27	113
Total	1	0	130	23	28

Variants in ATCAY

This is a list of pathogenic ClinVar variants found in the ATCAY region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-3880620-AC-A		Cayman type cerebellar ataxia	Likely benign (Jun 14, 2016)
19-3880652-C-A		Cayman type cerebellar ataxia	Likely benign (Jan 12, 2018)
19-3880660-A-G		Cayman type cerebellar ataxia	Benign (Jan 13, 2018)
19-3880675-G-T		Cayman type cerebellar ataxia	Uncertain significance (Jun 14, 2016)
19-3880809-C-T		Cayman type cerebellar ataxia	Benign (Jan 13, 2018)
19-3880852-C-G		Cayman type cerebellar ataxia	Uncertain significance (Jan 13, 2018)
19-3880874-C-T		Cayman type cerebellar ataxia	Uncertain significance (Mar 30, 2018)
19-3880880-C-A		Cayman type cerebellar ataxia	Uncertain significance (Jan 12, 2018)
19-3884705-G-A		Cayman type cerebellar ataxia	Uncertain significance (Mar 16, 2021)
19-3885714-G-A		Cayman type cerebellar ataxia	Uncertain significance (Jan 12, 2018)
19-3885778-C-T		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
19-3885803-C-T		Cayman type cerebellar ataxia	Conflicting classifications of pathogenicity (Mar 01, 2024)
19-3885826-A-T		Inborn genetic diseases	Uncertain significance (Dec 19, 2023)
19-3902504-C-T			Uncertain significance (Feb 01, 2022)
19-3902505-G-A			Likely benign (Oct 23, 2018)
19-3902506-G-A		Inborn genetic diseases	Uncertain significance (Jun 08, 2022)
19-3902507-G-A		Cayman type cerebellar ataxia • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jun 13, 2024)
19-3902528-C-T		Inborn genetic diseases	Uncertain significance (May 28, 2024)
19-3905423-T-C		Cayman type cerebellar ataxia	Likely benign (Apr 27, 2017)
19-3905449-T-C		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
19-3905459-C-T		Cayman type cerebellar ataxia	Conflicting classifications of pathogenicity (Jan 13, 2018)
19-3905496-G-C		Inborn genetic diseases	Uncertain significance (Jul 02, 2024)
19-3905498-G-A			Likely benign (Apr 12, 2018)
19-3905514-G-A		Inborn genetic diseases	Uncertain significance (Jul 26, 2024)
19-3905527-G-C		Inborn genetic diseases	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATCAY	protein_coding	protein_coding	ENST00000450849	12	48216

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.621	0.379	124629	0	6	124635	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	185	258	0.718	0.0000178	2451
Missense in Polyphen		64	110.22	0.58063		1023
Synonymous	-0.414	116	110	1.05	0.00000892	692
Loss of Function	3.38	4	20.5	0.195	8.77e-7	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000646
Ashkenazi Jewish	0.0000998	0.0000994
East Asian	0.00	0.00
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.0000192	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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