CAMTA1

Chr 1AD

calmodulin binding transcription activator 1

Also known as: CANPMR, CECBA

NCBI Gene: 23261ENSG00000171735UniProt: Q9Y6Y1OMIM: 611501

The CAMTA1 protein is a transcription factor containing DNA-binding domains, ankyrin repeats, and calmodulin-binding motifs that functions in the nucleus. Loss-of-function mutations cause autosomal dominant cerebellar dysfunction with variable cognitive and behavioral abnormalities. The gene is highly intolerant to loss-of-function variants, supporting haploinsufficiency as the mechanism of disease.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismADLOEUF 0.171 OMIM phenotype
Clinical Summary— CAMTA1
🧬
Gene-Disease Validity (ClinGen)
cerebellar dysfunction with variable cognitive and behavioral abnormalities · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
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
30 unique Pathogenic / Likely Pathogenic· 181 VUS of 300 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint
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
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
LoF OE0.09 (0.05–0.17)
0≤0.351.4
Missense OE0.71 (0.67–0.76)
0≤0.61.4
Synonymous OE0.96
0≤1.21.6
LoF obs/exp: 7 / 76.6Missense obs/exp: 725 / 1017.9Syn Z: 0.71
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveCAMTA1-related cerebellar dysfunction with variable cognitive and behavioural abnormalitiesLOFAD
DN
0.2997th %ile
GOF
0.3094th %ile
LOF
0.80top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 1 literature citation · 73% of P/LP variants are LoF · LOEUF 0.17

Literature Evidence

LOFHere, we show that global or nervous system deletion of CAMTA1 in mice causes severe ataxia with Purkinje cell degeneration and cerebellar atrophy, partially resembling the consequences of haploinsufficiency of the human CAMTA1 locus.PMID:25049392

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

300 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic19
Likely Pathogenic11
VUS181
Likely Benign60
Benign1
Conflicting2
19
Pathogenic
11
Likely Pathogenic
181
VUS
60
Likely Benign
1
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
13
0
6
0
19
Likely Pathogenic
9
2
0
0
11
VUS
5
166
9
1
181
Likely Benign
0
17
16
27
60
Benign
0
0
0
1
1
Conflicting
—2
Total271853129274

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.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Hypoxia‑induced exosomal CAMTA1 promotes radio‑resistance in MDA‑MB‑231 cells by regulating NRG1 to mediate M2 macrophage polarization.
Li Q et al.·Int J Oncol
2026Open Access
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
2025Open 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
2024Open 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
2024Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients