CAMTA2

calmodulin binding transcription activator 2, the group of IPT domain containing|Calmodulin binding transcription activators |MicroRNA protein coding host genes

Basic information

Region (hg38): 17:4967992-4987675

Links

ENSG00000108509 ∙ NCBI:23125 ∙ OMIM:611508 ∙ HGNC:18807 ∙ Uniprot:O94983 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAMTA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAMTA2 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				3	2	5
missense			68	1	1	70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding			2		1	3
Total	0	0	71	4	4

Variants in CAMTA2

This is a list of pathogenic ClinVar variants found in the CAMTA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4968744-G-A		not specified	Uncertain significance (Oct 13, 2023)
17-4968746-G-A		not specified	Uncertain significance (May 01, 2024)
17-4968771-C-G		not specified	Likely benign (Oct 27, 2022)
17-4968783-C-T		not specified	Uncertain significance (Mar 31, 2022)
17-4968798-G-A		not specified	Uncertain significance (Aug 30, 2021)
17-4968914-G-C		not specified	Uncertain significance (Dec 01, 2022)
17-4969643-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-4969648-A-G			Likely benign (Mar 01, 2024)
17-4969697-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-4969961-C-T		not specified	Uncertain significance (Jan 31, 2024)
17-4970078-G-A		not specified	Uncertain significance (Dec 13, 2021)
17-4970084-C-T		not specified	Uncertain significance (Jul 29, 2022)
17-4970344-G-C		not specified	Uncertain significance (Nov 17, 2022)
17-4970455-C-T		not specified	Uncertain significance (Jun 11, 2024)
17-4970467-C-T		not specified	Uncertain significance (Jan 04, 2022)
17-4970487-C-A		not specified	Uncertain significance (May 27, 2022)
17-4970503-C-T		not specified	Uncertain significance (Aug 14, 2023)
17-4970530-T-C		not specified	Uncertain significance (Apr 07, 2023)
17-4972328-C-G		not specified	Uncertain significance (Dec 13, 2022)
17-4972341-G-C		not specified	Uncertain significance (Jan 10, 2023)
17-4972396-C-G		not specified	Uncertain significance (Dec 06, 2022)
17-4972407-T-C		not specified	Conflicting classifications of pathogenicity (Feb 01, 2024)
17-4972425-G-A		not specified	Uncertain significance (Feb 22, 2023)
17-4972486-C-A		not specified	Uncertain significance (Feb 16, 2023)
17-4972486-C-T		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAMTA2	protein_coding	protein_coding	ENST00000414043	23	19674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000825	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	627	746	0.840	0.0000451	7892
Missense in Polyphen		222	319.71	0.69438		3432
Synonymous	0.376	285	293	0.972	0.0000168	2697
Loss of Function	6.30	10	64.6	0.155	0.00000392	655

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000223	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000187	0.000185
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription activator. May act as tumor suppressor. {ECO:0000269|PubMed:11925432}.

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• loftool: 0.396
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.98

Haploinsufficiency Scores

• pHI: 0.322
• hipred: Y
• hipred_score: 0.613
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.883

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Camta2
• Phenotype: homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cardiac muscle hypertrophy in response to stress;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;protein binding;transcription factor binding;histone deacetylase binding;sequence-specific DNA binding