CAMTA1

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

Basic information

Region (hg38): 1:6785453-7769706

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 (Strong), 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 (338 variants)
• Cerebellar dysfunction with variable cognitive and behavioral abnormalities (96 variants)
• Inborn genetic diseases (55 variants)
• not specified (15 variants)
• CAMTA1-related condition (11 variants)
• Intellectual disability (7 variants)
• See cases (4 variants)
• Developmental disorder (2 variants)
• Neurodevelopmental disorder (2 variants)
• CAMTA1-Related Disorder (1 variants)
• Seizure;Intellectual disability (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.

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			2	76	23	101
missense	2	6	198	34	8	248
nonsense	9	15	1			25
start loss			1			1
frameshift	17	4	1			22
inframe indel			4	1		5
splice donor/acceptor (+/-2bp)	1	3	1			5
splice region		1	7	7	5	20
non coding	1		4	22	12	39
Total	30	28	212	133	43

Highest pathogenic variant AF is 0.00000657

Variants in CAMTA1

This is a list of pathogenic ClinVar variants found in the CAMTA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-6785531-A-G			Uncertain significance (Feb 28, 2020)
1-6785545-G-A			Likely benign (Jun 26, 2022)
1-6785569-C-T			Uncertain significance (Sep 30, 2019)
1-6785580-G-C			Uncertain significance (Jul 11, 2022)
1-6785584-C-T			Likely benign (Nov 15, 2022)
1-6785592-G-T			Likely benign (Oct 03, 2023)
1-6785593-A-G			Likely benign (Dec 12, 2023)
1-6807054-A-C			Likely benign (Mar 01, 2023)
1-6820184-G-A			Likely benign (Nov 01, 2022)
1-6820244-A-G		Inborn genetic diseases	Uncertain significance (Dec 14, 2022)
1-6825098-A-G		Neurodevelopmental abnormality	Likely benign (Apr 03, 2020)
1-6825129-C-G		Inborn genetic diseases	Uncertain significance (Jan 20, 2016)
1-6825130-T-A		Cerebellar dysfunction with variable cognitive and behavioral abnormalities	Uncertain significance (Apr 27, 2016)
1-6825140-A-G			Uncertain significance (Aug 09, 2022)
1-6825150-T-G		CAMTA1-related disorder	Likely benign (Sep 13, 2019)
1-6825153-ATGTC-A		Cerebellar dysfunction with variable cognitive and behavioral abnormalities	Pathogenic (Feb 24, 2022)
1-6825174-T-C			Benign (Oct 09, 2023)
1-6825177-A-G			Likely benign (Oct 13, 2023)
1-6825193-C-T			Uncertain significance (Dec 05, 2023)
1-6825205-A-G		Cerebellar dysfunction with variable cognitive and behavioral abnormalities	Uncertain significance (May 25, 2017)
1-6825207-T-G			Uncertain significance (May 27, 2022)
1-6825210-G-A			Likely pathogenic (Sep 16, 2022)
1-6825215-A-T		CAMTA1-related disorder	Benign (Dec 15, 2023)
1-6825223-C-CT			Benign (Aug 03, 2023)
1-6825226-T-C			Benign (Jan 21, 2024)

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