ACTR1A

actin related protein 1A, the group of Actin related proteins|Dynactin subunits

Basic information

Region (hg38): 10:102461881-102502712

Links

ENSG00000138107 ∙ NCBI:10121 ∙ OMIM:605143 ∙ HGNC:167 ∙ Uniprot:P61163 ∙ 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 ACTR1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACTR1A 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in ACTR1A

This is a list of pathogenic ClinVar variants found in the ACTR1A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-102471284-A-T		not specified	Uncertain significance (Oct 29, 2021)
10-102471332-G-A		not specified	Likely benign (Jul 06, 2021)
10-102473825-C-T			Likely benign (Dec 01, 2022)
10-102473849-G-C		not specified	Uncertain significance (Jul 08, 2021)
10-102482002-T-A		not specified	Uncertain significance (Oct 25, 2022)
10-102482123-A-G		not specified	Uncertain significance (Mar 12, 2024)
10-102484227-T-C		not specified	Uncertain significance (Mar 29, 2022)
10-102484230-A-T		not specified	Uncertain significance (Aug 17, 2022)
10-102484243-G-A		not specified	Uncertain significance (Mar 21, 2024)
10-102488184-T-C		not specified	Uncertain significance (Oct 12, 2022)
10-102489138-A-G		not specified	Likely benign (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACTR1A	protein_coding	protein_coding	ENST00000369905	11	23497

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.966	0.0338	125730	0	4	125734	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.03	100	229	0.437	0.0000141	2449
Missense in Polyphen		30	96.569	0.31066		1034
Synonymous	1.60	70	89.2	0.785	0.00000575	753
Loss of Function	3.94	3	23.7	0.126	0.00000148	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000390	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a multi-subunit complex involved in microtubule based vesicle motility. It is associated with the centrosome.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Regulation of PLK1 Activity at G2/M Transition;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;COPI-mediated anterograde transport;M Phase;Cell Cycle;ER to Golgi Anterograde Transport;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Intra-Golgi and retrograde Golgi-to-ER traffic;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.546

Intolerance Scores

• loftool: 0.266
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.304
• hipred: Y
• hipred_score: 0.749
• ghis: 0.599

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Actr1a

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;endoplasmic reticulum to Golgi vesicle-mediated transport;spermatogenesis;regulation of G2/M transition of mitotic cell cycle;vesicle-mediated transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;ciliary basal body-plasma membrane docking
• Cellular component: manchette;cytoplasm;centrosome;centriole;cytosol;dynactin complex;microtubule associated complex;microtubule cytoskeleton;COPI-coated vesicle;myelin sheath;extracellular exosome;cell cortex region
• Molecular function: protein binding;ATP binding