CTTN

cortactin

Basic information

Region (hg38): 11:70398404-70436584

Previous symbols: [ "EMS1" ]

Links

ENSG00000085733 ∙ NCBI:2017 ∙ OMIM:164765 ∙ HGNC:3338 ∙ Uniprot:Q14247 ∙ 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 CTTN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTTN 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				3	2	5
missense			57	4		61
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	7	2

Variants in CTTN

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

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

Position	Type	Phenotype	Significance	ClinVar
11-70407352-G-T		not specified	Uncertain significance (Apr 12, 2024)
11-70407370-G-C		not specified	Uncertain significance (Dec 20, 2021)
11-70409836-A-G		not specified	Uncertain significance (Dec 14, 2022)
11-70409849-G-C		not specified	Uncertain significance (Dec 01, 2022)
11-70409913-C-T		not specified	Uncertain significance (May 28, 2024)
11-70414543-C-T		not specified	Uncertain significance (Oct 07, 2024)
11-70414593-G-A		not specified	Uncertain significance (Jul 30, 2024)
11-70417019-C-G		not specified	Uncertain significance (Mar 03, 2022)
11-70417032-C-T			Likely benign (Dec 04, 2017)
11-70417037-A-G		not specified	Uncertain significance (May 17, 2023)
11-70417040-A-G		not specified	Uncertain significance (Oct 20, 2024)
11-70417045-G-A		not specified	Uncertain significance (Dec 03, 2021)
11-70417045-G-C		not specified	Uncertain significance (Nov 08, 2024)
11-70417067-A-G		not specified	Uncertain significance (Feb 01, 2025)
11-70419755-A-G		not specified	Uncertain significance (Apr 18, 2023)
11-70419766-G-A		not specified	Uncertain significance (Jan 06, 2023)
11-70419823-C-A		not specified	Uncertain significance (Aug 19, 2023)
11-70420447-C-A		not specified	Uncertain significance (Aug 27, 2024)
11-70420482-G-T		not specified	Uncertain significance (Dec 05, 2022)
11-70422946-C-G		not specified	Uncertain significance (Mar 20, 2023)
11-70422954-T-G		not specified	Uncertain significance (Dec 18, 2023)
11-70422957-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-70422960-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-70422974-G-A			Benign (Jan 08, 2018)
11-70422984-C-T		not specified	Uncertain significance (Mar 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTTN	protein_coding	protein_coding	ENST00000376561	17	38181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0892	0.911	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.868	352	401	0.878	0.0000256	4147
Missense in Polyphen		143	200.61	0.71281		2070
Synonymous	-0.479	182	174	1.05	0.0000134	1168
Loss of Function	4.34	10	39.4	0.254	0.00000203	435

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to the organization of the actin cytoskeleton and cell shape (PubMed:21296879). Plays a role in the formation of lamellipodia and in cell migration. Plays a role in the regulation of neuron morphology, axon growth and formation of neuronal growth cones (By similarity). Through its interaction with CTTNBP2, involved in the regulation of neuronal spine density (By similarity). Plays a role in the invasiveness of cancer cells, and the formation of metastases (PubMed:16636290). Plays a role in focal adhesion assembly and turnover (By similarity). In complex with ABL1 and MYLK regulates cortical actin-based cytoskeletal rearrangement critical to sphingosine 1-phosphate (S1P)-mediated endothelial cell (EC) barrier enhancement (PubMed:20861316). Plays a role in intracellular protein transport and endocytosis, and in modulating the levels of potassium channels present at the cell membrane (PubMed:17959782). Plays a role in receptor-mediated endocytosis via clathrin-coated pits (By similarity). Required for stabilization of KCNH1 channels at the cell membrane (PubMed:23144454). {ECO:0000250|UniProtKB:Q60598, ECO:0000250|UniProtKB:Q66HL2, ECO:0000269|PubMed:16636290, ECO:0000269|PubMed:17959782, ECO:0000269|PubMed:21296879, ECO:0000269|PubMed:23144454}.
• Pathway: Tight junction - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathogenic Escherichia coli infection;Hepatitis C and Hepatocellular Carcinoma;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Fibroblast growth factor-1;RHO GTPases activate PAKs;RHO GTPase Effectors;Signaling by Rho GTPases;Clathrin-mediated endocytosis;EGFR1;agrin in postsynaptic differentiation;N-cadherin signaling events;PDGFR-beta signaling pathway;FGF signaling pathway;E-cadherin signaling in the nascent adherens junction;Syndecan-3-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.586

Intolerance Scores

• loftool: 0.542
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.251
• hipred: Y
• hipred_score: 0.662
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.798

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cttn
• Phenotype: embryo phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: intracellular protein transport;receptor-mediated endocytosis;substrate-dependent cell migration, cell extension;actin filament polymerization;regulation of axon extension;positive regulation of actin filament polymerization;actin cytoskeleton reorganization;positive regulation of smooth muscle contraction;focal adhesion assembly;neuron projection morphogenesis;cell motility;membrane organization;dendritic spine maintenance;lamellipodium organization;regulation of autophagy of mitochondrion;negative regulation of extrinsic apoptotic signaling pathway
• Cellular component: ruffle;podosome;cytoplasm;Golgi apparatus;cytosol;cytoskeleton;actin filament;plasma membrane;clathrin-coated pit;focal adhesion;cell cortex;voltage-gated potassium channel complex;lamellipodium;growth cone;cortical cytoskeleton;dendritic spine;intracellular membrane-bounded organelle;mitotic spindle midzone
• Molecular function: protein binding;profilin binding;cadherin binding