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.

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.

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				1		1
missense			43			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	1	0

Variants in PACSIN3

This is a list of pathogenic ClinVar variants found in the PACSIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47177936-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-47177977-C-T		not specified	Uncertain significance (Oct 16, 2023)
11-47177995-C-T		not specified	Uncertain significance (Jan 11, 2023)
11-47178402-C-T		not specified	Uncertain significance (Apr 23, 2024)
11-47178408-C-A		not specified	Uncertain significance (Sep 03, 2024)
11-47178457-T-G		not specified	Uncertain significance (Jan 26, 2022)
11-47178903-C-T		not specified	Uncertain significance (Jan 23, 2025)
11-47178924-G-A		not specified	Uncertain significance (May 23, 2024)
11-47178925-C-T		not specified	Uncertain significance (Feb 10, 2022)
11-47178927-G-T		not specified	Uncertain significance (Jan 16, 2024)
11-47178979-G-A		not specified	Uncertain significance (May 09, 2024)
11-47178998-G-C		not specified	Uncertain significance (Dec 21, 2022)
11-47179015-T-A		not specified	Uncertain significance (Dec 28, 2023)
11-47179239-C-A		not specified	Uncertain significance (Feb 20, 2025)
11-47179263-G-A		not specified	Uncertain significance (Nov 13, 2023)
11-47179484-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-47179490-C-T		not specified	Uncertain significance (May 03, 2023)
11-47179491-G-A			Likely benign (Sep 01, 2022)
11-47179493-C-T		not specified	Uncertain significance (Apr 12, 2024)
11-47179522-T-A		not specified	Uncertain significance (Dec 26, 2023)
11-47179538-G-A		not specified	Uncertain significance (Jul 07, 2024)
11-47179565-T-C		not specified	Uncertain significance (Jul 09, 2024)
11-47180199-T-C		not specified	Uncertain significance (Jan 07, 2025)
11-47180232-C-T		not specified	Uncertain significance (Aug 01, 2024)
11-47180233-G-A		not specified	Uncertain significance (Oct 03, 2024)

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