CAMTA1

Chr 1AD

calmodulin binding transcription activator 1

Also known as: CANPMR, CECBA

NCBI Gene: 23261ENSG00000171735UniProt: Q9Y6Y1

The protein encoded by this gene contains a CG1 DNA-binding domain, a transcription factor immunoglobulin domain, ankyrin repeats, and calmodulin-binding IQ motifs. The encoded protein is thought to be a transcription factor and may be a tumor suppressor. However, a translocation event is sometimes observed between this gene and the WWTR1 gene, with the resulting WWTR1-CAMTA1 oncoprotein leading to epithelioid hemangioendothelioma, a malignant vascular cancer. [provided by RefSeq, Mar 2017]

Primary Disease Associations & Inheritance

Cerebellar dysfunction with variable cognitive and behavioral abnormalitiesMIM #614756
AD
1027
ClinVar variants
53
Pathogenic / LP
1.00
pLI score· haploinsufficient
0
Active trials
Clinical Summary— CAMTA1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
53 Pathogenic / Likely Pathogenic· 309 VUS of 1027 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.17LOEUF
pLI 1.000
Z-score 7.37
OE 0.09 (0.05–0.17)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
3.26Z-score
OE missense 0.71 (0.67–0.76)
725 obs / 1017.9 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.09 (0.05–0.17)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.71 (0.67–0.76)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.96
0≤1.21.6
LoF obs/exp: 7 / 76.6Missense obs/exp: 725 / 1017.9Syn Z: 0.71

ClinVar Variant Classifications

1027 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic32
Likely Pathogenic21
VUS309
Likely Benign101
Benign4
Conflicting7
32
Pathogenic
21
Likely Pathogenic
309
VUS
101
Likely Benign
4
Benign
7
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
11
0
21
0
32
Likely Pathogenic
14
3
4
0
21
VUS
4
284
19
2
309
Likely Benign
1
22
23
55
101
Benign
0
1
2
1
4
Conflicting
—7
Total303106958474

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CAMTA1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

CAMTA1-related cerebellar dysfunction with variable cognitive and behavioural abnormalities

definitive
ADLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗
splice region variantmissense variantstop gained NMD triggeringframeshift variant NMD triggering

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Cerebellar dysfunction with variable cognitive and behavioral abnormalities

MIM #614756

Molecular basis of disorder known

Autosomal dominant
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Penetrance, variable expressivity and monogenic neurodevelopmental disorders.
de Masfrand S et al.·Eur J Med Genet
2024
[Epithelioid hemangioendothelioma].
Cousin S et al.·Bull Cancer
2019Review
Hepatic Epithelioid Hemangioendothelioma.
Studer LL et al.·Arch Pathol Lab Med
2018Review
Expanding the molecular spectrum and the neurological phenotype related to CAMTA1 variants.
Jacobs EZ et al.·Clin Genet
2021
The role of Calmodulin Binding Transcription Activator 1 (CAMTA1) gene and its putative genetic partners in the human nervous system.
Alves G et al.·Psychogeriatrics
2022Review
The natural history of progressive myoclonus ataxia.
van der Veen S et al.·Neurobiol Dis
2024Natural history
The genetics of vascular tumours: an update.
Torrence D et al.·Histopathology
2022Review
Epithelioid hemangioendothelioma-its history, clinical features, molecular biology and current therapy.
Tsuchihashi K et al.·Jpn J Clin Oncol
2024Review
Malignant vascular tumors--an update.
Antonescu C·Mod Pathol
2014Review
The oncogenic fusion protein TAZ::CAMTA1 promotes genomic instability and senescence through hypertranscription.
Neil E et al.·Commun Biol
2023
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
CAMTA1 Nonsense Variant Inherited From Asymptomatic Mother: Extremely Variable Expressivity in Congenital Ataxia.
Lee SY et al.·Clin Genet
2026
CAMTA1-immunonegative epithelioid hemangioendotheliomas of the liver: a clinicopathological and molecular analysis of seven cases.
Nie Y et al.·Front Oncol
2025🔓 Open AccessCohort
Circ-CAMTA1 regulated by Ca2+ influx inhibited pyruvate carboxylase activity and modulate T cell function in patients with systemic lupus erythematosus.
Yu HC et al.·Arthritis Res Ther
2024🔓 Open AccessCohort
Retraction: Long noncoding RNA CAMTA1 promotes proliferation and mobility of the human breast cancer cell line MDA-MB-231 via targeting miR-20b.
Oncology Research Editorial Office.·Oncol Res
2024🔓 Open Access
Primary pulmonary epithelioid hemangioendothelioma metastatic to the pleura and mediastinal lymph node with a prominent rhabdoid cytomorphology showing CAMTA1::WWTR1 fusion and novel PRDM1 and TNFRSF14 mutations.
Gonzalez MF et al.·Cytopathology
2024
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools