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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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ALPK3
alpha kinase 3
Chromosome 15 Β· 15q25.3
NCBI Gene: 57538Ensembl: ENSG00000136383.8HGNC: HGNC:17574UniProt: Q96L96
24PubMed Papers
21Diseases
0Drugs
267Pathogenic Variants
FUNCTIONAL ROLE
Kinase
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
heart developmentcardiac muscle cell developmentnucleuscardiac muscle cell differentiationhypertrophic cardiomyopathyAbnormality of the cardiovascular systemcardiomyopathyNeurodevelopmental disorder
✦AI Summary

ALPK3 encodes alpha-protein kinase 3, a non-sarcomeric protein involved in cardiomyocyte differentiation and cardiac muscle development 1. Functionally, ALPK3 appears critical for normal myocardial development, as loss-of-function variants disrupt cardiomyocyte organization and contractile function. Biallelic damaging ALPK3 variants cause pediatric-onset cardiomyopathy with distinctive pathophysiology: most patients initially present with neonatal dilated cardiomyopathy (44.4%) that transitions to ventricular hypertrophy during disease progression 1. Histopathologically, affected myocardium shows focal cardiomyocyte hypertrophy, subendocardial fibroelastosis, myofibrillar disarray, extensive myocardial fibrosis, and myocyte vacuolation 12. Most biallelic cases exhibit extracardiac manifestations including musculoskeletal abnormalities (contractures, scoliosis), craniofacial features (cleft palate, facial dysmorphisms), and webbed neck 13. Heterozygous ALPK3 truncating variants are pathogenic causes of autosomal dominant hypertrophic cardiomyopathy, occurring in 1.56% of HCM patients with significantly elevated odds ratios 2. ALPK3 truncating variants associate with apical/concentric hypertrophy patterns and short PR intervals, with myocardial outcomes comparable to sarcomere gene-positive patients 24. Recent ClinGen curation classified ALPK3 as having strong evidence for autosomal dominant and definitive evidence for autosomal recessive HCM 5. Intermediate-effect missense variants in ALPK3 contribute to approximately 4.8% of HCM genetic burden and modify disease severity 6.

Sources cited
1
Biallelic ALPK3 variants cause pediatric cardiomyopathy with neonatal DCM transitioning to hypertrophy; histopathology shows focal cardiomyocyte hypertrophy, fibroelastosis, and myofibrillar disarray; extracardiac features including contractures, scoliosis, cleft palate, and craniofacial dysmorphisms are common
PMID: 32480058
2
Heterozygous ALPK3 truncating variants are pathogenic and autosomal dominant, occurring in 1.56% of HCM patients with elevated odds ratios; associated with apical/concentric hypertrophy patterns, short PR intervals, myocardial fibrosis, and myocyte vacuolation
PMID: 34263907
3
ALPK3-related pediatric cardiomyopathy presents with progressive left ventricular hypertrophy, craniofacial-skeletal abnormalities, and electrocardiographic changes including prolonged QT intervals; disease often transitions from DCM to HCM
PMID: 34645221
4
ALPK3 has strong evidence for autosomal dominant HCM association and definitive evidence for autosomal recessive inheritance
PMID: 39132495
5
ALPK3 mutations predominantly associate with apical hypertrophy pattern in HCM patients, distinct from other genetic variants
PMID: 37561025
6
Intermediate-effect ALPK3 missense variants contribute approximately 4.8% of HCM genetic burden and modify disease severity and outcomes
PMID: 40879562
Disease Associationsβ“˜21
hypertrophic cardiomyopathyOpen Targets
0.82Strong
Abnormality of the cardiovascular systemOpen Targets
0.57Moderate
cardiomyopathyOpen Targets
0.53Moderate
Neurodevelopmental disorderOpen Targets
0.43Moderate
hypothyroidismOpen Targets
0.40Moderate
hydrops fetalisOpen Targets
0.37Weak
Non-immune hydrops fetalisOpen Targets
0.37Weak
Abnormality of the skeletal systemOpen Targets
0.35Weak
familial hypertrophic cardiomyopathyOpen Targets
0.34Weak
neurodegenerative diseaseOpen Targets
0.31Weak
esophageal ulcerOpen Targets
0.31Weak
thyroid diseaseOpen Targets
0.27Weak
Hashimoto's thyroiditisOpen Targets
0.26Weak
schizophreniaOpen Targets
0.20Weak
autism spectrum disorderOpen Targets
0.19Weak
mitral valve prolapseOpen Targets
0.18Weak
nephrotic syndromeOpen Targets
0.16Weak
Left ventricular noncompaction cardiomyopathyOpen Targets
0.11Weak
heart failureOpen Targets
0.10Suggestive
dilated cardiomyopathyOpen Targets
0.08Suggestive
Cardiomyopathy, familial hypertrophic, 27UniProt
Pathogenic Variants267
NM_020778.5(ALPK3):c.4130-1G>ALikely pathogenic
Cardiomyopathy, familial hypertrophic 27|not provided|Cardiovascular phenotype|Lung cancer
β˜…β˜…β˜†β˜†2026
NM_020778.5(ALPK3):c.1225C>T (p.Gln409Ter)Pathogenic
Cardiovascular phenotype|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 409
NM_020778.5(ALPK3):c.1093C>T (p.Gln365Ter)Pathogenic
not provided|Cardiomyopathy, familial hypertrophic 27
β˜…β˜…β˜†β˜†2026β†’ Residue 365
NM_020778.5(ALPK3):c.3175C>T (p.Arg1059Ter)Pathogenic
not provided|Cardiomyopathy, familial hypertrophic 27|Neurodevelopmental disorder|Cardiovascular phenotype|ALPK3-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 1059
NM_020778.5(ALPK3):c.3231_3232del (p.Asp1077fs)Pathogenic
not provided|Cardiovascular phenotype
β˜…β˜…β˜†β˜†2026β†’ Residue 1077
NM_020778.5(ALPK3):c.4213C>T (p.Arg1405Ter)Pathogenic
not provided|Cardiomyopathy|Cardiomyopathy, familial hypertrophic 27|Cardiovascular phenotype
β˜…β˜…β˜†β˜†2025β†’ Residue 1405
NM_020778.5(ALPK3):c.2237del (p.Gly746fs)Pathogenic
not provided|Cardiomyopathy, familial hypertrophic 27|Cardiovascular phenotype
β˜…β˜…β˜†β˜†2025β†’ Residue 746
NM_020778.5(ALPK3):c.2631_2634del (p.Ser878fs)Pathogenic
not provided|Cardiovascular phenotype|Cardiomyopathy, familial hypertrophic 27
β˜…β˜…β˜†β˜†2025β†’ Residue 878
NM_020778.5(ALPK3):c.4391del (p.Asn1464fs)Pathogenic
Hypertrophic cardiomyopathy|not provided|Cardiovascular phenotype|Cardiomyopathy, familial hypertrophic 27|Cardiomyopathy
β˜…β˜…β˜†β˜†2025β†’ Residue 1464
NM_020778.5(ALPK3):c.297del (p.Ile99fs)Pathogenic
Cardiomyopathy, familial hypertrophic 27|not provided|Cardiovascular phenotype|Primary familial hypertrophic cardiomyopathy
β˜…β˜…β˜†β˜†2025β†’ Residue 99
NM_020778.5(ALPK3):c.2043_2044delinsCT (p.Gln681_Glu682delinsHisTer)Pathogenic
not provided|Cardiomyopathy|Cardiovascular phenotype
β˜…β˜…β˜†β˜†2025β†’ Residue 681
NM_020778.5(ALPK3):c.1417del (p.Gln473fs)Pathogenic
Cardiomyopathy|not provided|Cardiovascular phenotype|ALPK3-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 473
NM_020778.5(ALPK3):c.1417dup (p.Gln473fs)Pathogenic
not provided|Cardiovascular phenotype
β˜…β˜…β˜†β˜†2025β†’ Residue 473
NM_020778.5(ALPK3):c.412C>T (p.Gln138Ter)Pathogenic
Hypertrophic cardiomyopathy|not provided|Cardiovascular phenotype|Cardiomyopathy, familial hypertrophic 27
β˜…β˜…β˜†β˜†2025β†’ Residue 138
NM_020778.5(ALPK3):c.3884G>A (p.Trp1295Ter)Pathogenic
not provided|Cardiovascular phenotype
β˜…β˜…β˜†β˜†2025β†’ Residue 1295
NM_020778.5(ALPK3):c.4234C>T (p.Arg1412Ter)Pathogenic
not provided|Cardiovascular phenotype|Cardiomyopathy, familial hypertrophic 27
β˜…β˜…β˜†β˜†2025β†’ Residue 1412
NM_020778.5(ALPK3):c.3726del (p.Lys1243fs)Pathogenic
Hypertrophic cardiomyopathy|not provided|Cardiomyopathy, familial hypertrophic 27|Cardiomyopathy
β˜…β˜…β˜†β˜†2025β†’ Residue 1243
NM_020778.5(ALPK3):c.3340C>T (p.Arg1114Ter)Pathogenic
not provided|Cardiovascular phenotype|Cardiomyopathy, familial hypertrophic 27
β˜…β˜…β˜†β˜†2025β†’ Residue 1114
NM_020778.5(ALPK3):c.386_389del (p.Thr129fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 129
NM_020778.5(ALPK3):c.2668C>T (p.Gln890Ter)Pathogenic
not provided|Cardiomyopathy, familial hypertrophic 27
β˜…β˜…β˜†β˜†2025β†’ Residue 890
View on ClinVar β†—
Related Genes
EIF2AK3Protein interaction79%PAX4Protein interaction71%CSRP3Co-mentioned in literature40%FHOD3Co-mentioned in literature40%LRRC10Shared pathway33%SMYD4Shared pathway33%
Tissue Expression6 tissues
Heart
100%
Lung
9%
Brain
8%
Liver
4%
Ovary
1%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
ALPK3EIF2AK3PAX4CSRP3FHOD3LRRC10SMYD4
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q96L96
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.87LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.74 [0.63–0.87]
RankingsWhere ALPK3 stands among ~20K protein-coding genes
  • #13,138of 20,598
    Most Researched24
  • #237of 5,498
    Most Pathogenic Variants267 Β· top 5%
  • #7,734of 17,882
    Most Constrained (LOEUF)0.87
Genes detectedALPK3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Expanding the clinical and genetic spectrum of ALPK3 variants: Phenotypes identified in pediatric cardiomyopathy patients and adults with heterozygous variants.
PMID: 32480058
Am Heart J Β· 2020
1.00
2
Minor hypertrophic cardiomyopathy genes, major insights into the genetics of cardiomyopathies.
PMID: 34526680
Nat Rev Cardiol Β· 2022
0.90
3
Alpha-protein kinase 3 (ALPK3) truncating variants are a cause of autosomal dominant hypertrophic cardiomyopathy.
PMID: 34263907
Eur Heart J Β· 2021
0.80
4
[ALPK3 gene-related pediatric cardiomyopathy with craniofacial-skeletal features: a report and literature review].
PMID: 34645221
Zhonghua Er Ke Za Zhi Β· 2021
0.70
5
Genes Associated With HypertrophicΒ Cardiomyopathy: A Reappraisal by the ClinGen Hereditary Cardiovascular Disease Gene Curation Expert Panel.
PMID: 39971408
J Am Coll Cardiol Β· 2025
0.60