TTF2

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

Basic information

Region (hg38): 1:117060325-117107453

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.

• Inborn genetic diseases (39 variants)
• not provided (19 variants)

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.

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	4	6
missense			36	8	8	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	10	12

Variants in TTF2

This is a list of pathogenic ClinVar variants found in the TTF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-117060369-A-G		not specified	Uncertain significance (Jul 09, 2021)
1-117060509-G-A			Benign (Sep 11, 2018)
1-117060524-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-117062405-C-G		not specified	Uncertain significance (Feb 12, 2024)
1-117073677-A-G		not specified	Uncertain significance (Jul 12, 2022)
1-117073701-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-117074974-C-A		not specified	Uncertain significance (Dec 17, 2023)
1-117074976-A-G			Benign (Dec 31, 2019)
1-117075060-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-117075062-G-A		not specified	Uncertain significance (May 10, 2023)
1-117075065-C-G			Likely benign (May 25, 2018)
1-117075091-G-C		not specified	Uncertain significance (Jul 26, 2022)
1-117075168-A-G		not specified	Uncertain significance (Jan 24, 2023)
1-117075222-A-G			Benign (May 31, 2018)
1-117075232-T-G		not specified	Likely benign (Aug 10, 2021)
1-117075281-T-C		not specified	Uncertain significance (Apr 13, 2022)
1-117075365-C-A		not specified	Uncertain significance (Nov 17, 2022)
1-117075376-A-C		not specified	Uncertain significance (Feb 12, 2024)
1-117075402-G-C			Benign (Dec 31, 2019)
1-117075419-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-117075435-A-T		not specified	Uncertain significance (Dec 06, 2021)
1-117075441-C-T		not specified	Uncertain significance (May 16, 2022)
1-117075473-G-A		not specified	Uncertain significance (Jun 26, 2023)
1-117075531-G-A		not specified	Likely benign (Jan 10, 2022)
1-117075557-C-G		not specified	Uncertain significance (Oct 25, 2022)

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

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