CYTIP

cytohesin 1 interacting protein, the group of PDZ domain containing

Basic information

Region (hg38): 2:157414618-157488961

Previous symbols: [ "PSCDBP" ]

Links

ENSG00000115165 ∙ NCBI:9595 ∙ OMIM:604448 ∙ HGNC:9506 ∙ Uniprot:O60759 ∙ 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 CYTIP gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYTIP 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in CYTIP

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

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

Position	Type	Phenotype	Significance	ClinVar
2-157415709-G-A		not specified	Uncertain significance (Dec 02, 2022)
2-157415803-C-G		not specified	Uncertain significance (Jun 03, 2022)
2-157415907-A-G		not specified	Uncertain significance (Oct 27, 2022)
2-157415931-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-157415942-C-T		not specified	Uncertain significance (Mar 29, 2022)
2-157415976-A-G		not specified	Uncertain significance (Mar 20, 2023)
2-157416048-G-A		not specified	Uncertain significance (Nov 18, 2022)
2-157416069-G-A		not specified	Uncertain significance (Jan 24, 2024)
2-157416110-A-G		not specified	Uncertain significance (Sep 17, 2021)
2-157418529-G-T		not specified	Uncertain significance (Jan 23, 2024)
2-157418543-T-C		not specified	Uncertain significance (Oct 25, 2022)
2-157427380-C-T		not specified	Uncertain significance (Nov 09, 2021)
2-157427382-G-A		not specified	Uncertain significance (Jun 11, 2021)
2-157430900-T-C		not specified	Uncertain significance (Mar 14, 2023)
2-157430928-G-C		not specified	Uncertain significance (Oct 12, 2021)
2-157434718-A-C		not specified	Uncertain significance (Oct 04, 2022)
2-157443912-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-157443927-C-T		not specified	Uncertain significance (Jun 30, 2022)
2-157443935-G-A		not specified	Uncertain significance (Oct 26, 2021)
2-157443956-G-A		not specified	Uncertain significance (Dec 15, 2022)
2-157443985-A-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYTIP	protein_coding	protein_coding	ENST00000264192	8	74343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00212	0.994	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.631	180	205	0.876	0.0000116	2364
Missense in Polyphen		47	66.954	0.70197		717
Synonymous	0.416	73	77.7	0.940	0.00000447	673
Loss of Function	2.54	8	20.4	0.393	0.00000121	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000525	0.000525
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000902	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: By its binding to cytohesin-1 (CYTH1), it modifies activation of ARFs by CYTH1 and its precise function may be to sequester CYTH1 in the cytoplasm.
• Pathway: Amplification and Expansion of Oncogenic Pathways as Metastatic Traits (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.680
• rvis_EVS: -0.74
• rvis_percentile_EVS: 13.94

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.418
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cytip
• Phenotype: hematopoietic system phenotype; neoplasm; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: regulation of cell adhesion
• Cellular component: nucleoplasm;cytoplasm;early endosome;cytosol;cell cortex
• Molecular function: protein binding