CYTH4

cytohesin 4, the group of Pleckstrin homology domain containing|Cytohesins

Basic information

Region (hg38): 22:37282027-37315341

Previous symbols: [ "PSCD4" ]

Links

ENSG00000100055 ∙ NCBI:27128 ∙ OMIM:606514 ∙ HGNC:9505 ∙ Uniprot:Q9UIA0 ∙ 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 CYTH4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYTH4 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			26	3	2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	3

Variants in CYTH4

This is a list of pathogenic ClinVar variants found in the CYTH4 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37282585-C-A		not specified	Uncertain significance (Aug 01, 2024)
22-37292623-C-G		not specified	Uncertain significance (Oct 04, 2024)
22-37292627-C-A		not specified	Uncertain significance (Dec 05, 2024)
22-37292639-G-A		not specified	Uncertain significance (May 22, 2023)
22-37292641-G-A		EBV-positive nodal T- and NK-cell lymphoma • not specified	Uncertain significance (Aug 07, 2024)
22-37296051-A-G			Benign (Jun 05, 2018)
22-37297591-C-T			Benign (Jun 05, 2018)
22-37297606-G-A		not specified	Likely benign (Mar 15, 2024)
22-37297631-A-G		not specified	Uncertain significance (Mar 07, 2024)
22-37297639-G-A		not specified	Uncertain significance (Nov 14, 2024)
22-37297648-A-C			Benign (Jun 05, 2018)
22-37299238-C-A		not specified	Uncertain significance (Feb 28, 2023)
22-37299245-G-A		not specified	Uncertain significance (Nov 17, 2022)
22-37300909-A-T		not specified	Uncertain significance (Mar 25, 2024)
22-37300911-T-C		not specified	Uncertain significance (Sep 07, 2022)
22-37300968-G-A		not specified	Likely benign (Apr 07, 2023)
22-37300969-C-T		not specified	Uncertain significance (Jun 16, 2023)
22-37303356-A-G		not specified	Uncertain significance (Nov 24, 2024)
22-37303358-C-T		not specified	Uncertain significance (Oct 21, 2021)
22-37303359-G-A		not specified	Uncertain significance (Sep 13, 2023)
22-37303370-A-G		not specified	Likely benign (Apr 18, 2023)
22-37303401-G-A		not specified	Uncertain significance (Nov 07, 2023)
22-37309263-G-A		not specified	Uncertain significance (Aug 16, 2021)
22-37311478-T-C		not specified	Uncertain significance (Jul 06, 2021)
22-37312024-G-A		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYTH4	protein_coding	protein_coding	ENST00000248901	13	33315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000773	0.999	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	199	264	0.753	0.0000178	2628
Missense in Polyphen		62	110.21	0.56255		1069
Synonymous	0.961	95	108	0.882	0.00000790	709
Loss of Function	2.97	10	26.5	0.378	0.00000145	270

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes guanine-nucleotide exchange on ARF1 and ARF5. Promotes the activation of ARF factors through replacement of GDP with GTP. {ECO:0000269|PubMed:10652308}.
• 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;Intra-Golgi traffic;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.543
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.243
• hipred: Y
• hipred_score: 0.575
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyth4

Gene ontology

• Biological process: regulation of ARF protein signal transduction
• Cellular component: Golgi membrane;cytosol;plasma membrane
• Molecular function: ARF guanyl-nucleotide exchange factor activity;lipid binding