PACSIN3

protein kinase C and casein kinase substrate in neurons 3, the group of F-BAR domain containing |MicroRNA protein coding host genes

Basic information

Region (hg38): 11:47177522-47186443

Links

ENSG00000165912

∙ NCBI:29763 ∙ OMIM:606513 ∙ HGNC:8572 ∙ Uniprot:Q9UKS6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

myopathy (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PACSIN3 gene.

not_specified (78 variants)
CONGENITAL_MYOPATHY_27 (3 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PACSIN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016223.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			77 clinvar	1 clinvar		78
nonsense	1 clinvar					1
start loss						0
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)						0
Total	3	0	77	2	0

Highest pathogenic variant AF is 0.000018698975

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PACSIN3	protein_coding	protein_coding	ENST00000539589	9	8919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00189	0.997	125708	0	36	125744	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.776	256	293	0.872	0.0000209	2763
Missense in Polyphen		81	111.37	0.72733		1118
Synonymous	0.623	108	117	0.927	0.00000808	809
Loss of Function	2.90	9	24.5	0.368	0.00000122	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000606	0.000602
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.000219	0.000217
South Asian	0.0000982	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a role in endocytosis and regulates internalization of plasma membrane proteins. Overexpression impairs internalization of SLC2A1/GLUT1 and TRPV4 and increases the levels of SLC2A1/GLUT1 and TRPV4 at the cell membrane. Inhibits the TRPV4 calcium channel activity (By similarity). {ECO:0000250, ECO:0000269|PubMed:11082044}.;
Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis (Consensus)

Recessive Scores

pRec: 0.202

Intolerance Scores

loftool: 0.738
rvis_EVS: -0.53
rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

pHI: 0.491
hipred: Y
hipred_score: 0.694
ghis: 0.636

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.849

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pacsin3
Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); hematopoietic system phenotype; skeleton phenotype;

Zebrafish Information Network

Gene name: pacsin3
Affected structure: post-vent region
Phenotype tag: abnormal
Phenotype quality: bent

Gene ontology

Biological process: endocytosis;cytoskeleton organization;negative regulation of endocytosis;positive regulation of membrane protein ectodomain proteolysis;negative regulation of calcium ion transport;plasma membrane tubulation
Cellular component: cytoplasm;cytosol;cytoskeleton;plasma membrane;extracellular exosome
Molecular function: protein binding;phospholipid binding;cytoskeletal protein binding;lipid binding;calcium channel inhibitor activity