TTF1

transcription termination factor 1, the group of Myb/SANT domain containing

Basic information

Region (hg38): 9:132375548-132406851

Links

ENSG00000125482 ∙ NCBI:7270 ∙ OMIM:600777 ∙ HGNC:12397 ∙ Uniprot:Q15361 ∙ 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 TTF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTF1 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	2	4
missense			60	8	3	71
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	62	10	5

Variants in TTF1

This is a list of pathogenic ClinVar variants found in the TTF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-132375926-A-C		not specified	Uncertain significance (Jan 20, 2023)
9-132375929-G-A		not specified	Uncertain significance (Mar 13, 2023)
9-132375934-T-C		not specified	Uncertain significance (Dec 08, 2023)
9-132375949-C-T		not specified	Uncertain significance (May 09, 2023)
9-132375973-C-T		not specified	Uncertain significance (Nov 21, 2023)
9-132375974-ATGGCGCC-A			Uncertain significance (Sep 01, 2021)
9-132375990-G-T		not specified	Uncertain significance (Jun 06, 2023)
9-132376076-G-A		not specified	Uncertain significance (Oct 26, 2022)
9-132376109-T-G		not specified	Uncertain significance (May 08, 2024)
9-132376144-G-A		not specified	Uncertain significance (Oct 12, 2021)
9-132379074-T-C		not specified	Uncertain significance (Mar 16, 2022)
9-132379074-T-G		not specified	Uncertain significance (Jan 06, 2023)
9-132379115-T-G		not specified	Uncertain significance (May 27, 2022)
9-132379139-A-G		not specified	Uncertain significance (Nov 12, 2021)
9-132386605-C-T		not specified	Uncertain significance (Dec 14, 2021)
9-132388154-A-G		not specified	Uncertain significance (Jan 23, 2023)
9-132388164-G-A		not specified	Uncertain significance (Jun 01, 2023)
9-132388191-G-T		not specified	Uncertain significance (Apr 20, 2024)
9-132390681-C-T		not specified	Uncertain significance (Jun 28, 2023)
9-132390775-C-T		not specified	Uncertain significance (Oct 26, 2022)
9-132390792-T-C		not specified	Uncertain significance (May 14, 2024)
9-132390795-C-T		not specified	Likely benign (Sep 12, 2023)
9-132390822-C-G		not specified	Uncertain significance (Mar 08, 2024)
9-132392075-C-G		Hypothyroidism, congenital, nongoitrous, 2	Uncertain significance (Mar 29, 2024)
9-132392106-C-T		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTF1	protein_coding	protein_coding	ENST00000334270	10	31202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.21e-13	0.821	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.107	476	483	0.986	0.0000257	5987
Missense in Polyphen		61	78.088	0.78117		996
Synonymous	-0.548	189	180	1.05	0.0000104	1654
Loss of Function	1.85	25	37.2	0.673	0.00000208	469

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000549	0.000549
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000211	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.000238	0.000229
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. Plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. Interaction with BAZ2A/TIP5 recovers DNA-binding activity. {ECO:0000269|PubMed:7597036}.
• Pathway: Thyroid hormone synthesis - Homo sapiens (human);Human Thyroid Stimulating Hormone (TSH) signaling pathway;ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);Surfactant metabolism;Metabolism of proteins;RNA Polymerase I Promoter Clearance;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation (Consensus)

Recessive Scores

• pRec: 0.0867

Intolerance Scores

• loftool: 0.944
• rvis_EVS: 1.27
• rvis_percentile_EVS: 93.67

Haploinsufficiency Scores

• pHI: 0.389
• hipred: N
• hipred_score: 0.343
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttf1

Gene ontology

• Biological process: DNA-templated transcription, termination;termination of RNA polymerase I transcription;negative regulation of DNA replication;cellular protein metabolic process
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol;plasma membrane
• Molecular function: DNA binding;chromatin binding