CAMTA1

calmodulin binding transcription activator 1, the group of Calmodulin binding transcription activators |IPT domain containing

Basic information

Region (hg38): 1:6785454-7769706

Links

ENSG00000171735

∙ NCBI:23261 ∙ OMIM:611501 ∙ HGNC:18806 ∙ Uniprot:Q9Y6Y1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

cerebellar dysfunction with variable cognitive and behavioral abnormalities (Definitive), mode of inheritance: AD
cerebellar dysfunction with variable cognitive and behavioral abnormalities (Definitive), mode of inheritance: AD
cerebellar dysfunction with variable cognitive and behavioral abnormalities (Supportive), mode of inheritance: AD
cerebellar dysfunction with variable cognitive and behavioral abnormalities (Strong), mode of inheritance: AD
cerebellar dysfunction with variable cognitive and behavioral abnormalities (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cerebellar ataxia, nonprogressive, with mental retardation	AD	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	22693284

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAMTA1 gene.

not_provided (559 variants)
Inborn_genetic_diseases (160 variants)
Cerebellar_dysfunction_with_variable_cognitive_and_behavioral_abnormalities (142 variants)
CAMTA1-related_disorder (51 variants)
not_specified (20 variants)
Intellectual_disability (10 variants)
See_cases (4 variants)
Neurodevelopmental_abnormality (3 variants)
Neurodevelopmental_disorder (2 variants)
Neurodevelopmental_disorder_with_coarse_facies_and_mild_distal_skeletal_abnormalities (2 variants)
Developmental_disorder (2 variants)
Epilepsy (1 variants)
Hereditary_ataxia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAMTA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015215.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	4 clinvar	133 clinvar	19 clinvar	157
missense	4 clinvar	10 clinvar	392 clinvar	67 clinvar	5 clinvar	478
nonsense	12 clinvar	18 clinvar	1 clinvar			31
start loss			1			1
frameshift	28 clinvar	11 clinvar	2 clinvar			41
splice donor/acceptor (+/-2bp)	1 clinvar	12 clinvar	2 clinvar			15
Total	45	52	402	200	24

Highest pathogenic variant AF is 0.000008227157

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAMTA1	protein_coding	protein_coding	ENST00000303635	23	984383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.58e-8	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.26	725	1.02e+3	0.712	0.0000652	11017
Missense in Polyphen		302	480.25	0.62884		5301
Synonymous	0.711	417	436	0.957	0.0000326	3288
Loss of Function	7.37	7	76.6	0.0913	0.00000413	835

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000248	0.000231
European (Non-Finnish)	0.0000464	0.0000439
Middle Eastern	0.000110	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcriptional activator. May act as a tumor suppressor. {ECO:0000269|PubMed:11925432, ECO:0000269|PubMed:15709179}.;
Disease: DISEASE: Cerebellar ataxia, non-progressive, with mental retardation (CANPMR) [MIM:614756]: A neurodevelopmental disorder characterized by mildly delayed psychomotor development, early onset of cerebellar ataxia, and intellectual disability later in childhood and adult life. Other features may include neonatal hypotonia, dysarthria, and dysmetria. Brain imaging in some patients shows cerebellar atrophy. Dysmorphic facial features are variable. {ECO:0000269|PubMed:22693284}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: miR-targeted genes in muscle cell - TarBase (Consensus)

Intolerance Scores

loftool: 0.00455
rvis_EVS: -2.13
rvis_percentile_EVS: 1.5

Haploinsufficiency Scores

pHI: 0.236
hipred: Y
hipred_score: 0.693
ghis: 0.609

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.705

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Camta1
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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive 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); growth/size/body region phenotype;

Gene ontology

Biological process: positive regulation of protein dephosphorylation;positive regulation of transcription by RNA polymerase II;neuromuscular process controlling balance;positive regulation of calcineurin-NFAT signaling cascade
Cellular component: nucleus;nucleolus;cytosol
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding