ACVR1C

activin A receptor type 1C, the group of Type 1 receptor serine/threonine kinases

Basic information

Region (hg38): 2:157526767-157628864

Links

ENSG00000123612 ∙ NCBI:130399 ∙ OMIM:608981 ∙ HGNC:18123 ∙ Uniprot:Q8NER5 ∙ 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 ACVR1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACVR1C 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				2	5	7
missense			18	1	3	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					21	21
Total	0	0	18	3	29

Variants in ACVR1C

This is a list of pathogenic ClinVar variants found in the ACVR1C region.

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

Position	Type	Phenotype	Significance	ClinVar
2-157533929-A-T		not specified	Uncertain significance (Dec 28, 2023)
2-157533941-C-T		ACVR1C-related disorder	Benign (Jul 12, 2019)
2-157533956-T-C			Benign (Apr 19, 2019)
2-157533979-G-C		not specified	Uncertain significance (Dec 21, 2023)
2-157534017-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-157534114-C-T			Benign (Jun 18, 2021)
2-157534254-G-A			Benign (Jun 19, 2021)
2-157538301-T-C			Benign (Nov 10, 2018)
2-157538407-T-C			Benign (Jun 19, 2021)
2-157538567-C-G			Benign (Jun 09, 2021)
2-157538579-A-G			Likely benign (Dec 31, 2019)
2-157538753-A-G			Benign (Jun 18, 2021)
2-157541093-C-T		not specified	Uncertain significance (May 11, 2022)
2-157542526-G-C			Benign (Jun 18, 2021)
2-157542743-T-C		not specified	Uncertain significance (Jul 21, 2021)
2-157542786-C-T		ACVR1C-related disorder	Benign (May 28, 2019)
2-157542812-T-C		not specified	Uncertain significance (Dec 28, 2022)
2-157542998-T-A			Benign (Nov 10, 2018)
2-157543002-G-T			Benign (Jun 18, 2021)
2-157543065-G-A			Benign (Jun 18, 2021)
2-157544202-ATT-A			Benign (Jun 18, 2021)
2-157544202-A-AT			Benign (Jun 18, 2021)
2-157544294-C-A			Benign (Nov 10, 2018)
2-157544396-C-T			Benign (Nov 10, 2018)
2-157544441-A-G		ACVR1C-related disorder	Benign (Sep 17, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACVR1C	protein_coding	protein_coding	ENST00000243349	9	102239

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000852	0.999	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	198	267	0.742	0.0000134	3174
Missense in Polyphen		70	133.44	0.5246		1627
Synonymous	0.0706	96	96.9	0.991	0.00000516	962
Loss of Function	3.00	10	26.7	0.374	0.00000156	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000255	0.000246
Middle Eastern	0.00	0.00
South Asian	0.0000717	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine protein kinase which forms a receptor complex on ligand binding. The receptor complex consisting of 2 type II and 2 type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators, SMAD2 and SMAD3. Receptor for activin AB, activin B and NODAL. Plays a role in cell differentiation, growth arrest and apoptosis. {ECO:0000269|PubMed:12063393, ECO:0000269|PubMed:15531507}.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);TGF-Core;Developmental Biology;Regulation of signaling by NODAL;Signal Transduction;Signaling by Activin;Signaling by NODAL;Signaling by TGF-beta family members (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.0761
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.759
• hipred: Y
• hipred_score: 0.635
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.765

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acvr1c
• Phenotype: normal phenotype

Gene ontology

• Biological process: response to dietary excess;protein phosphorylation;transforming growth factor beta receptor signaling pathway;pattern specification process;response to glucose;lipid storage;cell differentiation;apoptotic nuclear changes;response to insulin;activin receptor signaling pathway;nodal signaling pathway;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of insulin secretion;negative regulation of trophoblast cell migration;negative regulation of chorionic trophoblast cell proliferation
• Cellular component: plasma membrane;integral component of plasma membrane;receptor complex;activin receptor complex
• Molecular function: protein serine/threonine kinase activity;transforming growth factor beta-activated receptor activity;transforming growth factor beta receptor activity, type I;ATP binding;activin receptor activity, type I;growth factor binding;nodal binding;SMAD binding;metal ion binding;activin binding