CYTH1

cytohesin 1, the group of Cytohesins|Pleckstrin homology domain containing

Basic information

Region (hg38): 17:78674048-78782297

Previous symbols: [ "PSCD1" ]

Links

ENSG00000108669 ∙ NCBI:9267 ∙ OMIM:182115 ∙ HGNC:9501 ∙ Uniprot:Q15438 ∙ 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 CYTH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYTH1 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			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in CYTH1

This is a list of pathogenic ClinVar variants found in the CYTH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-78676098-C-T		not specified	Uncertain significance (Sep 16, 2022)
17-78680215-T-C		not specified	Uncertain significance (Dec 13, 2022)
17-78680978-T-C		not specified	Uncertain significance (Sep 16, 2022)
17-78680996-C-T		not specified	Uncertain significance (May 27, 2022)
17-78692445-T-C		not specified	Uncertain significance (May 29, 2024)
17-78698294-G-C		not specified	Uncertain significance (Sep 20, 2023)
17-78698373-T-C		not specified	Uncertain significance (Mar 31, 2024)
17-78698819-C-G			Uncertain significance (Apr 04, 2024)
17-78698863-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-78698942-T-C		not specified	Uncertain significance (Jul 14, 2021)
17-78698950-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-78701742-A-T		not specified	Uncertain significance (Mar 01, 2023)
17-78702138-C-G		not specified	Uncertain significance (May 02, 2024)
17-78702597-T-C		not specified	Uncertain significance (Jun 16, 2023)
17-78708229-A-T		not specified	Uncertain significance (Nov 04, 2022)
17-78708252-C-T		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYTH1	protein_coding	protein_coding	ENST00000361101	13	108250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000190	125587	0	2	125589	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	131	237	0.554	0.0000143	2657
Missense in Polyphen		25	69.095	0.36182		767
Synonymous	-0.512	96	89.8	1.07	0.00000563	695
Loss of Function	4.58	0	24.5	0.00	0.00000137	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
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, ARF5 and ARF6. Promotes the activation of ARF factors through replacement of GDP with GTP. Plays an important role in membrane trafficking, during junctional remodeling and epithelial polarization, through regulation of ARF6 activity. {ECO:0000250|UniProtKB:Q9QX11, ECO:0000269|PubMed:10652308, ECO:0000269|PubMed:29420262, ECO:0000269|PubMed:9653114}.
• 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;Class I PI3K signaling events;Intra-Golgi traffic;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.216

Intolerance Scores

• loftool: 0.380
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.231
• hipred: Y
• hipred_score: 0.775
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.856

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyth1
• 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: vesicle-mediated transport;regulation of cell adhesion;regulation of ARF protein signal transduction;establishment of epithelial cell polarity
• Cellular component: Golgi membrane;cytoplasm;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;lipid binding