CYTH3

cytohesin 3, the group of Cytohesins|Pleckstrin homology domain containing

Basic information

Region (hg38): 7:6161779-6272644

Previous symbols: [ "PSCD3" ]

Links

ENSG00000008256

∙ NCBI:9265 ∙ OMIM:605081 ∙ HGNC:9504 ∙ Uniprot:O43739 ∙ 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 CYTH3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYTH3 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			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in CYTH3

This is a list of pathogenic ClinVar variants found in the CYTH3 region.

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

Position	Phenotype	Significance	ClinVar
7-6164966-C-T	not specified	Uncertain significance (Jun 07, 2024)	3270736
7-6165275-G-C	not specified	Uncertain significance (Apr 07, 2022)	3079816
7-6165360-T-G	not specified	Uncertain significance (Dec 06, 2021)	2265173
7-6165552-C-T	not specified	Uncertain significance (Jan 02, 2024)	3079820
7-6173690-G-A	not specified	Uncertain significance (Dec 08, 2023)	3079818
7-6187083-C-T	not specified	Uncertain significance (Jul 19, 2023)	2612950
7-6187667-C-A	not specified	Uncertain significance (Aug 12, 2022)	2306820
7-6187691-T-C	not specified	Uncertain significance (Oct 05, 2023)	3079817
7-6187714-T-C	not specified	Uncertain significance (Aug 04, 2023)	2598654
7-6187715-T-G	not specified	Uncertain significance (Jan 31, 2022)	2274721
7-6190463-T-C	not specified	Uncertain significance (Jun 21, 2022)	2296118
7-6190480-C-T	not specified	Uncertain significance (Jan 02, 2024)	3079819
7-6190493-G-C	not specified	Uncertain significance (Apr 22, 2022)	2285144

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYTH3	protein_coding	protein_coding	ENST00000350796	13	110869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.723	0.277	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.57	133	247	0.539	0.0000155	2662
Missense in Polyphen		36	102.01	0.35292		1103
Synonymous	-2.15	127	99.6	1.27	0.00000714	701
Loss of Function	3.53	4	21.7	0.184	9.65e-7	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Promotes guanine-nucleotide exchange on ARF1 and ARF6. Promotes the activation of ARF factors through replacement of GDP with GTP. Play a role in the epithelial polarization (By similarity). {ECO:0000250|UniProtKB:O08967, ECO:0000269|PubMed:23940353, ECO:0000269|PubMed:9707577}.;
Pathway: Endocytosis - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Insulin Signaling;Vesicle-mediated transport;thrombin signaling and protease-activated receptors;Membrane Trafficking;adp-ribosylation factor;Class I PI3K signaling events;Intra-Golgi traffic;Arf6 signaling events;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.146

Intolerance Scores

loftool: 0.424
rvis_EVS: -0.54
rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

pHI: 0.128
hipred: Y
hipred_score: 0.685
ghis: 0.637

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.787

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cyth3
Phenotype

Gene ontology

Biological process: regulation of ARF protein signal transduction;positive regulation of cell adhesion;Golgi vesicle transport;establishment of epithelial cell polarity
Cellular component: Golgi membrane;ruffle;nucleoplasm;cytosol;plasma membrane;adherens junction;bicellular tight junction;extrinsic component of cytoplasmic side of plasma membrane
Molecular function: ARF guanyl-nucleotide exchange factor activity;protein binding;phosphatidylinositol-3,4,5-trisphosphate binding