CAMTA2

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the calmodulin-binding transcription activator protein family. Members of this family share a common domain structure that consists of a transcription activation domain, a DNA-binding domain, and a calmodulin-binding domain. The encoded protein may be a transcriptional coactivator of genes involved in cardiac growth. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jan 2010]

MANE transcript

NM_015099.4

Inheritance

—

ClinVar variants

U:196B:11

Top phenotype

Cerebellar dysfunction with variable cognitive and behavioral abnormalities

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr17:4,967,992-4,987,675

External References & Databases

Ensembl (ENSG00000108509)

Transcript & Mutation Effects

hg38 • Region Span ~19.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CAMTA2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 175

not providedTotal: 11

Cerebellar dysfunction with variable cognitive and behavioral abnormalitiesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015099.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	5 clinvar	2 clinvar	12
missense			178 clinvar	4 clinvar		182
nonsense			4 clinvar			4
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	196	9	2	207

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015099.4	RefSeq	NP_055914.2	22	MANE Select
ENST00000348066.8	Ensembl	ENSP00000321813.7	22	MANE Select
NM_001171166.2	RefSeq	NP_001164637.1	21	Standard
NM_001171167.2	RefSeq	NP_001164638.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
cardiac muscle hypertrophy in response to stress
positive regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
chromatin binding
protein binding
transcription factor binding
histone deacetylase binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000414043
Coding exons: 23
Length: 19674
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.55	627	746	0.840	0.0000451	7892
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.883

Gene Damage Prediction

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