TTF2

transcription termination factor 2, the group of Zinc fingers GRF-type|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:117060326-117107453

Links

ENSG00000116830

∙ NCBI:8458 ∙ OMIM:604718 ∙ HGNC:12398 ∙ Uniprot:Q9UNY4 ∙ 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 TTF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTF2 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2 clinvar	4 clinvar	6
missense			75 clinvar	11 clinvar	8 clinvar	94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	75	13	12

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTF2	protein_coding	protein_coding	ENST00000369466	23	47151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00e-22	0.769	125620	0	128	125748	0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.807	561	617	0.909	0.0000320	7548
Missense in Polyphen		175	191.47	0.91396		2366
Synonymous	-0.275	237	232	1.02	0.0000120	2273
Loss of Function	2.32	45	65.2	0.690	0.00000355	746

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00129	0.00129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000767	0.000761
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000573	0.000571
Middle Eastern	0.000767	0.000761
South Asian	0.000196	0.000196
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

Function: FUNCTION: DsDNA-dependent ATPase which acts as a transcription termination factor by coupling ATP hydrolysis with removal of RNA polymerase II from the DNA template. May contribute to mitotic transcription repression. May also be involved in pre-mRNA splicing. {ECO:0000269|PubMed:10455150, ECO:0000269|PubMed:12927788, ECO:0000269|PubMed:15125840, ECO:0000269|PubMed:9748214}.;
Pathway: Thyroid hormone synthesis - Homo sapiens (human);Human Thyroid Stimulating Hormone (TSH) signaling pathway (Consensus)

Recessive Scores

pRec: 0.0955

Intolerance Scores

loftool: 0.155
rvis_EVS: 1.43
rvis_percentile_EVS: 95.03

Haploinsufficiency Scores

pHI: 0.562
hipred: N
hipred_score: 0.383
ghis: 0.571

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.861

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ttf2
Phenotype

Gene ontology

Biological process: DNA-templated transcription, termination;termination of RNA polymerase II transcription;mRNA processing;RNA splicing
Cellular component: spliceosomal complex;cytosol;transcription elongation factor complex
Molecular function: DNA binding;helicase activity;protein binding;ATP binding;DNA-dependent ATPase activity;zinc ion binding