ACVRL1
protein-codingactivin A receptor like type 1, the group of Type 1 receptor serine/threonine kinases
Gene summary
This gene encodes a type I cell-surface receptor for the TGF-beta superfamily of ligands. It shares with other type I receptors a high degree of similarity in serine-threonine kinase subdomains, a glycine- and serine-rich region (called the GS domain) preceding the kinase domain, and a short C-terminal tail. The encoded protein, sometimes termed ALK1, shares similar domain structures with other closely related ALK or activin receptor-like kinase proteins that form a subfamily of receptor serine/threonine kinases. Mutations in this gene are associated with hemorrhagic telangiectasia type 2, also known as Rendu-Osler-Weber syndrome 2. [provided by RefSeq, Jul 2008]
- ACVRLK1
- ORW2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0010880
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0019180
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0010880
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0019180
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0010880
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0010880
Submitter: ClinGen
The relationship between *ACVRL1* and hereditary hemorrhagic telangiectasia, type 2 (HHT2), an autosomal dominant disorder, was evaluated using the ClinGen Clinical Validity Framework as of April 1, 2019. *ACVRL1* was first reported in relation to HHT2 in 1996 (Johnson et al., PMID: 8640225). HHT2 is evaluated by the presence of 3 or more of the Curacao criteria (PMID: 10751092). ACVRL1 is a type I TGF-β receptor and interacts with ENG in the TGF-β pathway. ENG is known to cause HHT1. The mechanism for disease is haploinsufficiency (PMID: 15879500) and at least 571 ACVRL1 variants, ranging from missense, in-frame indel to nonsense, frameshift, large deletions and whole gene deletions, have been reported in humans (http://www.arup.utah.edu/database/ACVRL1/ACVRL1_welcome.php). Evidence supporting this gene-disease relationship includes case-level data, segregation data and experimental data. Variants included in this curation come from 13 probands in 6 publications (PMIDs 86402252, 17384219, 26176610, 9245985 20364125, 20414677) and segregated with disease in 12 additional family members. More evidence is available in the literature, but the maximum score for genetic evidence evidence (12 pts) has been reached. This gene-disease relationship is also supported by animal models and in vitro functional assays. A number of mouse and zebra fish models have been developed for HHT (PMID: 17911384, 12588795, 24896812, 12050147). Additionally, interaction with the HHT-related gene *ENG* in the TGF-β pathway has been experimentally demonstrated (PMID: 15702480, 12015308). In summary, *ACVRL1* is definitively associated with autosomal dominant hereditary hemorrhagic telangiectasia, Type 2. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Hemostasis/Thrombosis Gene Curation Expert Panel on August 28, 2019 (SOP Version 6). Scoring was updated on 11/29/2022. Of note, pulmonary arterial hypertension (PAH) is a rare but severe complication of HHT2 that was independently evaluated as of June 9, 2021 by the Pulmonary Hypertension GCEP. More than 22 probands with rare, predicted deleterious *ACVRL1* variants have been reported (PMIDs:11484689, 14684682, 15065824, 20056902, 31727138 and others). Multiple variant types, including missense, have been reported and the carboxy terminus contains a conserved 11 amino acid NANDOR box in the protein kinase domain that shows enrichment of rare missense variants among PAH-HHT cases compared to HHT alone (PMID:20056902). Experimental evidence for a gene-disease relationship for HHT-PAH includes expression in pulmonary arterial endothelial cells and PAH plexiform lesions (PMID: 11484689), interaction with receptor ligand BMP10 (PMID: 17068149), and spontaneous pulmonary hypertension in an Acvrl1 knockout HHT mouse model (PMID: 21859819).
Inheritance Pattern: AD
Disease ID:MONDO:0010880
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Dermatologic; Gastrointestinal; Hematologic; Pulmonary
Intervention: Cardiovascular; Gastrointestinal; Hematologic; Obstetric; Pharmacogenomic; Pulmonary
Rationale: There are a number of surveillance/preventive/treatment based measures; These include: epistaxis treatment with humidification, lubricants, hormone therapy, anti-fibrinolytic agents, ablation, surgery, etc.; GI bleeding: iron replacement, hormonal or anti-fibrinolytic medication, surgery, etc.; Pulmonary AVM: catheter occlusion, and preventive measures such as antibiotic prophylaxis; symptomatic cerebral AVMs: surgery/embolotherapy, etc; Severe hepatic AVMs: liver transplantation if medical management fails; Specific pregnancy-related screening may be indicated; Anemia: Iron replacement or transfusion; Avoidance of certain activities and use of anticoagulant and anti-inflammatory agents (including aspirin) in the case of significant bleeding; For PAH, medical therapy (eg, prostanoids, endothelin receptor antagonists, etc.) may be beneficial, but lung transplantation may be indicated
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ACVRL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000020.3. 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 | 1 | 7 | 180 | 2 | 190 | |
| missense | 92 | 197 | 213 | 36 | 538 | |
| nonsense | 68 | 11 | 1 | 80 | ||
| start loss | 0 | |||||
| frameshift | 153 | 32 | 2 | 187 | ||
| splice donor/acceptor (+/-2bp) | 23 | 23 | 3 | 49 | ||
| Total | 336 | 264 | 226 | 216 | 2 | 1044 |
Highest pathogenic variant AF is 0.00003469516
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000011.2 | 9 | MANE Select | |
| Ensembl | ENSP00000373574.4 | 9 | MANE Select | |
| RefSeq | NP_001070869.1 | 9 | Standard | |
| RefSeq | NP_001393416.1 | 9 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| acvrl1 | Danio rerio | Structure: endothelial cell Quality: increased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- TGF-Core
- Signal Transduction
- TGF-beta super family signaling pathway canonical
- IL-7 signaling
- JAK STAT pathway and regulation
Biological Process
- angiogenesis
- response to hypoxia
- in utero embryonic development
- regulation of endothelial cell proliferation
- negative regulation of endothelial cell proliferation
Molecular Function
- protein serine/threonine kinase activity
- transmembrane receptor protein serine/threonine kinase activity
- transforming growth factor beta-activated receptor activity
- transforming growth factor beta receptor activity, type I
- protein binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- cell surface
- dendrite
- neuronal cell body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000388922
- Coding exons
- 9
- Length
- 16454
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 125745
- p
- 0.0000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.45 | 190 | 311 | 0.610 | 0.0000209 | 3227 |
| Missense (PolyPhen) | 57 | 153.08 | 0.37236 | 1576 | ||
| Synonymous | -0.449 | 145 | 138 | 1.05 | 0.00000978 | 1030 |
| Loss of Function | 2.66 | 9 | 22.7 | 0.397 | 0.00000108 | 243 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000080 | 0.000079 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Type I receptor for TGF-beta family ligands BMP9/GDF2 and BMP10 and important regulator of normal blood vessel development. On ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. May bind activin as well. {ECO:0000269|PubMed:22718755, ECO:0000269|PubMed:22799562, ECO:0000269|PubMed:26176610}.;
- Disease
- DISEASE: Telangiectasia, hereditary hemorrhagic, 2 (HHT2) [MIM:600376]: A multisystemic vascular dysplasia leading to dilation of permanent blood vessels and arteriovenous malformations of skin, mucosa, and viscera. The disease is characterized by recurrent epistaxis and gastro-intestinal hemorrhage. Visceral involvement includes arteriovenous malformations of the lung, liver, and brain. {ECO:0000269|PubMed:10694922, ECO:0000269|PubMed:10767348, ECO:0000269|PubMed:11170071, ECO:0000269|PubMed:11484689, ECO:0000269|PubMed:14684682, ECO:0000269|PubMed:15024723, ECO:0000269|PubMed:15712270, ECO:0000269|PubMed:16525724, ECO:0000269|PubMed:16752392, ECO:0000269|PubMed:20414677, ECO:0000269|PubMed:26176610, ECO:0000269|PubMed:8640225, ECO:0000269|PubMed:9245985}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.441
Intolerance Scores
- LoFtool
- 0.0783
- RVIS EVS
- -1.02
- RVIS percentile EVS
- 8
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |