TWF1

twinfilin actin binding protein 1

Basic information

Region (hg38): 12:43793723-43806328

Previous symbols: [ "PTK9" ]

Links

ENSG00000151239 ∙ NCBI:5756 ∙ OMIM:610932 ∙ HGNC:9620 ∙ Uniprot:Q12792 ∙ 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 TWF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TWF1 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in TWF1

This is a list of pathogenic ClinVar variants found in the TWF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-43795631-C-A		not specified	Uncertain significance (May 08, 2023)
12-43795634-A-C		not specified	Uncertain significance (Jan 06, 2023)
12-43795668-C-A		not specified	Uncertain significance (May 03, 2023)
12-43795679-T-C		not specified	Uncertain significance (Mar 25, 2024)
12-43795693-C-A		not specified	Uncertain significance (Apr 13, 2023)
12-43795695-T-C		not specified	Uncertain significance (Nov 08, 2022)
12-43795700-T-C		not specified	Uncertain significance (Oct 05, 2021)
12-43795704-C-T		not specified	Uncertain significance (Dec 07, 2024)
12-43795719-A-T		not specified	Uncertain significance (Aug 05, 2024)
12-43796993-T-C		not specified	Uncertain significance (Nov 21, 2023)
12-43797004-C-T		not specified	Uncertain significance (Dec 27, 2022)
12-43797010-A-G		not specified	Uncertain significance (Nov 17, 2022)
12-43797025-C-T		not specified	Uncertain significance (Dec 07, 2021)
12-43797052-C-T		not specified	Uncertain significance (Dec 16, 2023)
12-43797328-T-C		not specified	Uncertain significance (Apr 08, 2024)
12-43797346-A-C		not specified	Uncertain significance (Aug 17, 2022)
12-43797409-G-T		not specified	Uncertain significance (Apr 13, 2022)
12-43797763-T-C		not specified	Uncertain significance (Nov 10, 2024)
12-43797821-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-43798585-T-C		not specified	Uncertain significance (Feb 27, 2024)
12-43799418-G-C		not specified	Uncertain significance (Jun 18, 2021)
12-43799421-G-T		not specified	Uncertain significance (Sep 21, 2023)
12-43799442-G-C		not specified	Uncertain significance (Jun 06, 2023)
12-43799462-G-A		not specified	Uncertain significance (Apr 26, 2023)
12-43799474-T-G		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TWF1	protein_coding	protein_coding	ENST00000548315	10	12653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000209	0.978	125717	0	24	125741	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.919	147	182	0.808	0.00000878	2326
Missense in Polyphen		40	54.766	0.73038		681
Synonymous	0.778	54	61.8	0.874	0.00000275	647
Loss of Function	2.07	11	21.3	0.516	0.00000105	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000527	0.000526
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000936	0.0000924
European (Non-Finnish)	0.0000623	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Actin-binding protein involved in motile and morphological processes. Inhibits actin polymerization, likely by sequestering G-actin. By capping the barbed ends of filaments, it also regulates motility. Seems to play an important role in clathrin-mediated endocytosis and distribution of endocytic organelles (By similarity). {ECO:0000250}.
• Disease: DISEASE: Note=Defects in TWF1 has been found in a patient with isolated coloboma, a defect of the eye characterized by the absence of ocular structures due to abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). Isolated colobomas may be associated with an abnormally small eye (microphthalmia) or small cornea. {ECO:0000269|PubMed:28493397}.

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.496
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.391
• hipred: N
• hipred_score: 0.389
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.311

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Twf1
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of lamellipodium assembly;positive regulation of cardiac muscle hypertrophy;positive regulation of neuron projection development;peptidyl-tyrosine phosphorylation;actin filament depolymerization;negative regulation of actin filament polymerization;sequestering of actin monomers;regulation of actin phosphorylation;barbed-end actin filament capping
• Cellular component: cytoplasm;cytosol;actin filament;cell-cell junction;focal adhesion;actin cytoskeleton;myofibril;filopodium;ruffle membrane;perinuclear region of cytoplasm
• Molecular function: actin binding;actin monomer binding;protein tyrosine kinase activity;protein binding;ATP binding;phosphatidylinositol-4,5-bisphosphate binding;cadherin binding;actin filament binding