TCF20

transcription factor 20

Basic information

Region (hg38): 22:42160013-42343616

Links

ENSG00000100207

∙ NCBI:6942 ∙ OMIM:603107 ∙ HGNC:11631 ∙ Uniprot:Q9UGU0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

developmental delay with variable intellectual impairment and behavioral abnormalities (Strong), mode of inheritance: AD
developmental delay with variable intellectual impairment and behavioral abnormalities (Strong), mode of inheritance: AD
syndromic intellectual disability (Supportive), mode of inheritance: AD
developmental delay with variable intellectual impairment and behavioral abnormalities (Definitive), mode of inheritance: AD
developmental delay with variable intellectual impairment and behavioral abnormalities (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental delay with variable intellectual impairment and behavioral abnormalities	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	25228304; 27436265; 28135719; 30739909; 30819258

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TCF20 gene.

not_provided (858 variants)
Inborn_genetic_diseases (251 variants)
Developmental_delay_with_variable_intellectual_impairment_and_behavioral_abnormalities (162 variants)
TCF20-related_disorder (56 variants)
not_specified (43 variants)
Neurodevelopmental_abnormality (15 variants)
See_cases (6 variants)
Autism_spectrum_disorder (3 variants)
Intellectual_disability (3 variants)
Neurodevelopmental_delay (3 variants)
Intellectual_disability,_mild (2 variants)
Generalized_hypotonia (2 variants)
Autism (2 variants)
Intellectual_disability,_moderate (1 variants)
Attention_deficit_hyperactivity_disorder (1 variants)
Hypotonia (1 variants)
Autistic_behavior (1 variants)
Hypotelorism (1 variants)
Myoclonus (1 variants)
Craniosynostosis_syndrome (1 variants)
Ptosis (1 variants)
Global_developmental_delay (1 variants)
Pectus_excavatum (1 variants)
TCF20-related_neurodevelopmental_disorder (1 variants)
Developmental_disorder (1 variants)
Failure_to_thrive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCF20 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001378418.1. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	225 clinvar	26 clinvar	254
missense	1 clinvar	3 clinvar	533 clinvar	163 clinvar	25 clinvar	725
nonsense	36 clinvar	10 clinvar				46
start loss						0
frameshift	63 clinvar	20 clinvar	2 clinvar			85
splice donor/acceptor (+/-2bp)						0
Total	100	33	538	388	51

Highest pathogenic variant AF is 0.0000065748814

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCF20	protein_coding	protein_coding	ENST00000359486	4	183604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.98e-10	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0895	1048	1.06e+3	0.992	0.0000594	12835
Missense in Polyphen		331	409.88	0.80755		5106
Synonymous	-3.14	490	409	1.20	0.0000235	3975
Loss of Function	7.32	2	66.4	0.0301	0.00000368	795

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000553	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000176
Middle Eastern	0.0000553	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcriptional activator that binds to the regulatory region of MMP3 and thereby controls stromelysin expression. It stimulates the activity of various transcriptional activators such as JUN, SP1, PAX6 and ETS1, suggesting a function as a coactivator.;
Pathway: Matrix Metalloproteinases (Consensus)

Recessive Scores

pRec: 0.194

Intolerance Scores

loftool: 0.0597
rvis_EVS: -2.55
rvis_percentile_EVS: 0.85

Haploinsufficiency Scores

pHI: 0.332
hipred: N
hipred_score: 0.380
ghis: 0.558

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.602

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tcf20
Phenotype

Gene ontology

Biological process: regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
Cellular component: nucleus;nucleoplasm;nuclear body
Molecular function: DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;RNA binding;protein binding;transcription regulatory region DNA binding;metal ion binding