ACVR2A

activin A receptor type 2A, the group of Type 2 receptor serine/threonine kinases

Basic information

Region (hg38): 2:147844516-147930826

Previous symbols: [ "ACVR2" ]

Links

ENSG00000121989 ∙ NCBI:92 ∙ OMIM:102581 ∙ HGNC:173 ∙ Uniprot:P27037 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACVR2A gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACVR2A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in ACVR2A

This is a list of pathogenic ClinVar variants found in the ACVR2A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-147896391-C-T		not specified	Uncertain significance (Dec 21, 2023)
2-147899475-A-G		not specified	Uncertain significance (Feb 01, 2023)
2-147899762-C-G		not specified	Uncertain significance (Nov 21, 2022)
2-147899854-A-G		not specified	Uncertain significance (Feb 10, 2022)
2-147915329-A-G		not specified	Uncertain significance (Jun 06, 2023)
2-147917391-G-A		not specified	Uncertain significance (Jan 26, 2022)
2-147918525-G-C		not specified	Uncertain significance (Aug 15, 2023)
2-147920262-A-C		not specified	Uncertain significance (Oct 05, 2022)
2-147922983-G-A		not specified	Uncertain significance (Sep 01, 2021)
2-147927213-T-C		not specified	Uncertain significance (Jun 23, 2023)
2-147927215-G-T		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACVR2A	protein_coding	protein_coding	ENST00000241416	11	86308

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000279	125598	0	2	125600	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.29	123	277	0.444	0.0000133	3379
Missense in Polyphen		23	123.76	0.18584		1558
Synonymous	-0.167	98	95.9	1.02	0.00000483	947
Loss of Function	4.71	1	27.8	0.0359	0.00000137	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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. Receptor for activin A, activin B and inhibin A. Mediates induction of adipogenesis by GDF6 (By similarity). {ECO:0000250|UniProtKB:P27038, ECO:0000269|PubMed:1314589}.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Mesodermal Commitment Pathway;Developmental Biology;Regulation of signaling by NODAL;Signal Transduction;Signaling by Activin;TGF-beta super family signaling pathway canonical;Signaling by NODAL;IL-7 signaling;BMP Signalling Pathway;JAK STAT pathway and regulation;EPO signaling;BMP2 signaling TGF-beta MV;VEGF;Signaling by BMP;Signaling by TGF-beta family members;ALK1 signaling events (Consensus)

Recessive Scores

• pRec: 0.240

Intolerance Scores

• loftool: 0.0781
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.691
• hipred: Y
• hipred_score: 0.825
• ghis: 0.627

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.920

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Acvr2a
• Phenotype: respiratory system phenotype; embryo phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; skeleton phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: acvr2aa
• Affected structure: endochondral bone
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: gastrulation with mouth forming second;positive regulation of protein phosphorylation;protein phosphorylation;transmembrane receptor protein serine/threonine kinase signaling pathway;transforming growth factor beta receptor signaling pathway;spermatogenesis;determination of left/right symmetry;pattern specification process;mesoderm development;anterior/posterior pattern specification;positive regulation of pathway-restricted SMAD protein phosphorylation;positive regulation of bone mineralization;BMP signaling pathway;regulation of BMP signaling pathway;activin receptor signaling pathway;positive regulation of activin receptor signaling pathway;sperm ejaculation;penile erection;positive regulation of erythrocyte differentiation;positive regulation of osteoblast differentiation;positive regulation of transcription by RNA polymerase II;embryonic skeletal system development;regulation of nitric-oxide synthase activity;Sertoli cell proliferation;cellular response to BMP stimulus
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;cell surface;inhibin-betaglycan-ActRII complex;receptor complex;activin receptor complex
• 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 II;protein binding;ATP binding;coreceptor activity;activin-activated receptor activity;growth factor binding;PDZ domain binding;inhibin binding;type I transforming growth factor beta receptor binding;protein self-association;SMAD binding;metal ion binding;activin binding;BMP receptor activity