ANKRD1
protein-codingankyrin repeat domain 1, the group of Ankyrin repeat domain containing
Gene summary
The protein encoded by this gene is localized to the nucleus of endothelial cells and is induced by IL-1 and TNF-alpha stimulation. Studies in rat cardiomyocytes suggest that this gene functions as a transcription factor. Interactions between this protein and the sarcomeric proteins myopalladin and titin suggest that it may also be involved in the myofibrillar stretch-sensor system. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005045
Submitter: ClinGen
*ANKRD1* was first reported in relation to hypertrophic cardiomyopathy (HCM) in humans in 2009, where 2 unique missense variants were reported in probands with no family history of cardiomyopathy (Arimura T, et al., 2009, PMID: 19608031). *ANKRD1* has been associated with autosomal dominant HCM in 2 probands from 1 publication. Additional missense variants have been reported in humans, but either the frequency of the variants were too high, there were homozygotes present in gnomAD, the phenotypes more closely resembled DCM, or the probands had a variant in another HCM gene (Arimura T, et al., 2009, PMID: 1960803; Ng D, et al., 2013, PMID: 23861362; Cecconi M, et al., 2016, PMID: 27600940). This gene-disease relationship is supported by expression data, a cell culture model, and an animal model. High tissue specificity in the heart has been observed for this gene (Uhlén M, et al., 2015, PMID: 25613900). Expression studies in mature rat cardiomyocytes and the examination of contraction parameters using engineered heart tissues support the gene-disease association (Crocini C, et al., 2013, PMID: 23572067). Overexpression of ANKRD1 in mice with transverse aortic constriction was shown to exacerbate pathological cardiac remodeling through activation of the calcineurin/nuclear factor of activated T-cells pathway, a signaling pathway known to have an important role in cardiac hypertrophy (Chen C, et al., 2014, PMID: 25089522). This classification was originally approved by the ClinGen Hypertrophic Cardiomyopathy Gene Curation Expert Panel on September 19th, 2017, with a classification of limited. It was reevaluated by the ClinGen Hereditary Cardiovascular Disease Gene Curation Expert Panel on February 8th, 2023. As a result of this reevaluation, the classification was changed from limited to disputed.
Inheritance Pattern: AD
Disease ID:MONDO:0016333
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0015470
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0016333
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0024573
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0005453
Submitter: ClinGen
*ANKRD1* was first reported in relation to autosomal dominant congenital heart disease in 2022 (Yang et al., PMID: 30659708). One missense variant has been reported and is included in this curation (PMID: 30659708). This gene-disease relationship is also supported by evidence of *ANKRD1* expression in the human heart, protein interaction with NKX2.5, and a mouse model (overexpression of *ANKRD1*) that shows *ANKRD1* transgenic mice present with a sinus venosus defect. In summary, there is limited evidence supporting the relationship between ANKRD1 and autosomal dominant congenital heart disease. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen Congenital Heart Disease GCEP on the meeting date August 12th, 2024 (SOP Version 10)
Inheritance Pattern: AD
Disease ID:MONDO:0024573
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0005021
Submitter: ClinGen
ANKRD1 was originally evaluated for DXM by the ClinGen DCM GCEP on 08/12/2020. Evidence of the association of this gene with DCM was evaluated using SOP v10 on 02/07/2025. As a result, the classification did not change. A summary of the information contributing to the classification of this gene at the time of re-evaluation is summarized herein. ANKRD1 was first reported in relation to autosomal dominant DCM in 2009 (Duboscq-Bidot L et al, 2009, PMID: 19525294). Human genetic evidence supporting this gene-disease relationship includes case level data and segregation data. At least 16 unique variants (missense (n=13) and nonsense (n=3)) have been reported in humans, representing at least 23 probands from 7 publications (Duboscq-Bidot L et al, 2009, PMID: 19525294; Moulik et al, 2009, PMID: 19608030, Dalin et al, 2017, PMID: 27886618, Haas et al, 2015, PMID: 25163546, Marschall C et al, 2019, PMID: 31737537, Zhang XL et al, 2020, PMID: 32041989, van Lint et. al 2019, PMID: 30847666). Variants in this gene segregated with disease in 4 additional family members (Duboscq-Bidot L et al, 2009, PMID: 19525294). In addition, this gene-disease association is supported by evidence from expression studies (Duboscq-Bidot L et al, 2009, PMID: 19525294; Moulik et al, 2009, PMID: 19608030), in vitro functional assays (Moulik et al, 2009, PMID: 19608030), and non-human models (Zheng et al, 2021, PMID: 33734499). In summary, there is limited evidence to support this gene-disease relationship. More evidence is needed to support the relationship of ANKRD1 with autosomal dominant DCM. This classification was approved by the ClinGen Dilated Cardiomyopathy Working Group on 02/07/2025 (SOP Version 10).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ANKRD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014391.3. 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 | 4 | 78 | 1 | 83 | ||
| missense | 1 | 231 | 26 | 1 | 259 | |
| nonsense | 20 | 20 | ||||
| start loss | 3 | 3 | ||||
| frameshift | 16 | 16 | ||||
| splice donor/acceptor (+/-2bp) | 10 | 10 | ||||
| Total | 0 | 1 | 284 | 104 | 2 | 391 |
Highest pathogenic variant AF is 0.0000049571395
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055206.2 | 9 | MANE Select | |
| Ensembl | ENSP00000360762.3 | 9 | MANE Select | |
| Ensembl | ENSP00000539757.1 | 8 | Standard | |
| Ensembl | ENSP00000539757.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
- Glucocorticoid Receptor Pathway
- Nuclear Receptors Meta-Pathway
- Hypertrophy Model
Biological Process
- negative regulation of transcription by RNA polymerase II
- regulation of transcription by RNA polymerase II
- skeletal muscle tissue development
- positive regulation of neuron projection development
- regulation of lipid metabolic process
Molecular Function
- RNA polymerase II transcription factor binding
- p53 binding
- DNA binding
- transcription coactivator activity
- transcription corepressor activity
Cellular Component
- fibrillar center
- nucleus
- nucleoplasm
- transcription factor complex
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371697
- Coding exons
- 9
- Length
- 9181
- Individuals with no LoFs
- 125657
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 89
- Defined
- 125746
- p
- 0.000354
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.193 | 166 | 173 | 0.959 | 0.0000101 | 2085 |
| Missense (PolyPhen) | 56 | 55.972 | 1.0005 | 674 | ||
| Synonymous | 0.339 | 63 | 66.5 | 0.947 | 0.00000448 | 588 |
| Loss of Function | 0.474 | 16 | 18.2 | 0.880 | 0.00000107 | 228 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00062 | rare |
| Latino/Admixed American | 0.00067 | 0.00067 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00039 | 0.00038 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00036 | 0.00035 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play an important role in endothelial cell activation. May act as a nuclear transcription factor that negatively regulates the expression of cardiac genes. Induction seems to be correlated with apoptotic cell death in hepatoma cells. {ECO:0000269|PubMed:15805281, ECO:0000269|PubMed:7730328}.;
- Disease
- DISEASE: Total anomalous pulmonary venous return (TAPVR) [MIM:106700]: Rare congenital heart disease (CHD) in which the pulmonary veins fail to connect to the left atrium during cardiac development, draining instead into either the right atrium or one of its venous tributaries. This disease accounts for 1.5% of all CHDs and has a prevalence of approximately 1 out of 15'000 live births. {ECO:0000269|PubMed:18273862}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- LoFtool
- 0.821
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.76
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.996
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |