ACVRL1

protein-coding

activin 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]

Previous symbols:
  • ACVRLK1
  • ORW2

MANE transcript

NM_000020.3

Inheritance

AD, AR

ClinVar variants

P:600U:226B:218

Top phenotype

Telangiectasia, hereditary hemorrhagic, type 2

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr12:51,906,908-51,923,361

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~16.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

telangiectasia, hereditary hemorrhagic, type 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010880

Submitter: PanelApp Australia

hereditary hemorrhagic telangiectasiaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019180

Submitter: Ambry Genetics

telangiectasia, hereditary hemorrhagic, type 2DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0010880

Submitter: G2P

hereditary hemorrhagic telangiectasiaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019180

Submitter: Orphanet

telangiectasia, hereditary hemorrhagic, type 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010880

Submitter: Genomics England PanelApp

telangiectasia, hereditary hemorrhagic, type 2DEFINITIVE

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).

telangiectasia, hereditary hemorrhagic, type 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010880

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Telangiectasia, hereditary hemorrhagic, type 2AD

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

Refs: 5037289; 3186989; 8640225; 10946360; 9354504; 11170071; 11484689; 14684682; 16470787; 16155196; 6542389; 17786384; 18498373; 18831062; 18312453; 19439755; 20056902; 20301525Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ACVRL1 variants in ClinVar

22 Conditions Cataloged
Telangiectasia, hereditary hemorrhagic, type 2Total: 875
Cardiovascular phenotypeTotal: 479
not providedTotal: 260
ACVRL1-related disorderTotal: 117
not specifiedTotal: 99
Pulmonary arterial hypertension related to hereditary hemorrhagic telangiectasiaTotal: 30
Hereditary hemorrhagic telangiectasiaTotal: 26
Pulmonary hypertension, primary, 1Total: 14

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
7
clinvar
180
clinvar
2
clinvar
190
missense
92
clinvar
197
clinvar
213
clinvar
36
clinvar
538
nonsense
68
clinvar
11
clinvar
1
clinvar
80
start loss
0
frameshift
153
clinvar
32
clinvar
2
clinvar
187
splice donor/acceptor (+/-2bp)
23
clinvar
23
clinvar
3
clinvar
49
Total33626422621621044

Highest pathogenic variant AF is 0.00003469516

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000020.3RefSeqNP_000011.29MANE Select
ENST00000388922.9EnsemblENSP00000373574.49MANE Select
NM_001077401.2RefSeqNP_001070869.19Standard
NM_001406487.1RefSeqNP_001393416.19Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
acvrl1Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.451903110.6100.00002093227
Missense (PolyPhen)57153.080.372361576
Synonymous-0.4491451381.050.000009781030
Loss of Function2.66922.70.3970.00000108243

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000800.000079rare
South Asian0.0000340.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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