CYTH2

cytohesin 2, the group of Pleckstrin homology domain containing|Cytohesins

Basic information

Region (hg38): 19:48469208-48482314

Previous symbols: [ "PSCD2L", "PSCD2" ]

Links

ENSG00000105443 ∙ NCBI:9266 ∙ OMIM:602488 ∙ HGNC:9502 ∙ Uniprot:Q99418 ∙ 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 CYTH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYTH2 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in CYTH2

This is a list of pathogenic ClinVar variants found in the CYTH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48469516-C-A		not specified	Uncertain significance (Jun 11, 2024)
19-48470448-G-C		not specified	Uncertain significance (Oct 20, 2021)
19-48470484-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-48470493-G-A		not specified	Uncertain significance (Jul 27, 2024)
19-48470496-G-A		not specified	Uncertain significance (May 30, 2024)
19-48470635-T-C		not specified	Uncertain significance (Jun 07, 2023)
19-48472347-A-G		not specified	Uncertain significance (Jun 23, 2023)
19-48472370-G-A		not specified	Uncertain significance (Apr 20, 2024)
19-48472383-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-48473972-G-A		not specified	Uncertain significance (May 16, 2022)
19-48474269-G-A		not specified	Uncertain significance (Jun 26, 2024)
19-48474926-G-A		not specified	Uncertain significance (May 23, 2024)
19-48478471-G-A		not specified	Uncertain significance (Mar 21, 2023)
19-48478573-G-A		not specified	Uncertain significance (Oct 12, 2022)
19-48479130-G-A		not specified	Uncertain significance (Oct 03, 2024)
19-48479164-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-48479188-A-G		not specified	Uncertain significance (Jul 13, 2022)
19-48479191-A-G		not specified	Uncertain significance (Dec 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYTH2	protein_coding	protein_coding	ENST00000452733	12	13283

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.255	0.745	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	160	257	0.622	0.0000169	2623
Missense in Polyphen		23	65.233	0.35258		714
Synonymous	-0.420	110	105	1.05	0.00000672	756
Loss of Function	3.54	6	25.1	0.239	0.00000150	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000898	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a guanine-nucleotide exchange factor (GEF). Promotes guanine-nucleotide exchange on ARF1, ARF3 and ARF6. Activates ARF factors through replacement of GDP with GTP (By similarity). The cell membrane form, in association with ARL4 proteins, recruits ARF6 to the plasma membrane (PubMed:17398095). Involved in neurite growth (By similarity). {ECO:0000250|UniProtKB:P63034, ECO:0000269|PubMed:17398095}.
• Pathway: Endocytosis - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Vesicle-mediated transport;thrombin signaling and protease-activated receptors;Membrane Trafficking;adp-ribosylation factor;Arf1 pathway;Class I PI3K signaling events;Intra-Golgi traffic;Arf6 signaling events;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.318
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.624
• hipred: Y
• hipred_score: 0.701
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.968

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyth2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: endocytosis;actin cytoskeleton organization;regulation of ARF protein signal transduction
• Cellular component: Golgi membrane;cytoplasm;cytosol;plasma membrane;adherens junction;bicellular tight junction;membrane;growth cone
• Molecular function: ARF guanyl-nucleotide exchange factor activity;protein binding;lipid binding;inositol 1,4,5 trisphosphate binding