PACSIN2

protein kinase C and casein kinase substrate in neurons 2, the group of F-BAR domain containing

Basic information

Region (hg38): 22:42835411-43015149

Links

ENSG00000100266 ∙ NCBI:11252 ∙ OMIM:604960 ∙ HGNC:8571 ∙ Uniprot:Q9UNF0 ∙ 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 PACSIN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PACSIN2 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in PACSIN2

This is a list of pathogenic ClinVar variants found in the PACSIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-42835477-T-A		not specified	Uncertain significance (Dec 19, 2023)
22-42840949-T-C		not specified	Uncertain significance (Mar 25, 2024)
22-42840961-C-T		not specified	Uncertain significance (Mar 21, 2023)
22-42840968-C-T		not specified	Uncertain significance (Dec 08, 2023)
22-42841008-T-C		not specified	Uncertain significance (Oct 04, 2022)
22-42847611-T-C		not specified	Uncertain significance (Nov 22, 2023)
22-42857140-G-A		not specified	Uncertain significance (Jan 08, 2024)
22-42871415-C-T		not specified	Uncertain significance (Mar 06, 2023)
22-42871443-C-T		not specified	Uncertain significance (Jan 31, 2024)
22-42871457-G-C		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
22-42871463-T-C		not specified	Uncertain significance (Sep 22, 2022)
22-42876199-A-G		not specified	Uncertain significance (Aug 10, 2021)
22-42876211-G-A		not specified	Uncertain significance (Nov 07, 2022)
22-42876256-G-A		not specified	Uncertain significance (Oct 30, 2023)
22-42876296-C-A		not specified	Uncertain significance (Jan 24, 2024)
22-42876304-T-C		not specified	Uncertain significance (Aug 21, 2023)
22-42876320-C-T		not specified	Uncertain significance (Mar 06, 2023)
22-42876915-C-G		not specified	Uncertain significance (Nov 29, 2021)
22-42879063-G-A		not specified	Uncertain significance (Jan 04, 2024)
22-42879128-C-G		not specified	Uncertain significance (Mar 21, 2024)
22-42882291-A-T		not specified	Uncertain significance (Aug 12, 2021)
22-42882299-T-G			Likely benign (Jul 01, 2022)
22-42890991-C-T		not specified	Uncertain significance (Sep 14, 2022)
22-42890992-G-A		not specified	Likely benign (Feb 21, 2024)
22-42891021-C-T		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PACSIN2	protein_coding	protein_coding	ENST00000263246	10	179734

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.213	0.787	125717	0	23	125740	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	248	313	0.793	0.0000202	3243
Missense in Polyphen		86	120.78	0.71205		1249
Synonymous	-0.346	140	135	1.04	0.0000101	853
Loss of Function	3.78	7	28.9	0.242	0.00000157	299

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.000509	0.000508
European (Non-Finnish)	0.0000709	0.0000703
Middle Eastern	0.000111	0.000109
South Asian	0.0000327	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid-binding protein that is able to promote the tubulation of the phosphatidic acid-containing membranes it preferentially binds. Plays a role in intracellular vesicle- mediated transport. Involved in the endocytosis of cell-surface receptors like the EGF receptor, contributing to its internalization in the absence of EGF stimulus. May also play a role in the formation of caveolae at the cell membrane. Recruits DNM2 to caveolae, and thereby plays a role in caveola-mediated endocytosis. {ECO:0000269|PubMed:21610094, ECO:0000269|PubMed:21693584, ECO:0000269|PubMed:23129763, ECO:0000269|PubMed:23236520, ECO:0000269|PubMed:23596323}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.207

Intolerance Scores

• loftool: 0.405
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.41

Haploinsufficiency Scores

• pHI: 0.248
• hipred: Y
• hipred_score: 0.756
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.736

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pacsin2
• Phenotype: homeostasis/metabolism phenotype; hearing/vestibular/ear 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); hematopoietic system phenotype; 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)

Gene ontology

• Biological process: cytoskeleton organization;actin cytoskeleton organization;protein localization to endosome;negative regulation of endocytosis;cell projection morphogenesis;modulation of chemical synaptic transmission;membrane organization;caveola assembly;caveolin-mediated endocytosis;plasma membrane tubulation
• Cellular component: cytoplasm;early endosome;cytosol;cytoskeleton;plasma membrane;caveola;cell-cell junction;focal adhesion;nuclear speck;extrinsic component of membrane;cytoplasmic vesicle membrane;ruffle membrane;intracellular membrane-bounded organelle;recycling endosome membrane;extracellular exosome;glutamatergic synapse
• Molecular function: transporter activity;protein binding;phospholipid binding;cytoskeletal protein binding;identical protein binding;cadherin binding;phosphatidic acid binding