TMF1

TATA element modulatory factor 1, the group of Golgins|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:69019827-69052339

Links

ENSG00000144747 ∙ NCBI:7110 ∙ OMIM:601126 ∙ HGNC:11870 ∙ Uniprot:P82094 ∙ 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 TMF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMF1 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				1		1
missense			56	3		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	4	0

Variants in TMF1

This is a list of pathogenic ClinVar variants found in the TMF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-69023188-T-C		not specified	Uncertain significance (Jun 29, 2023)
3-69023224-T-C		not specified	Uncertain significance (Sep 06, 2022)
3-69023317-A-T		not specified	Uncertain significance (Aug 14, 2023)
3-69024167-T-C		not specified	Uncertain significance (Dec 21, 2022)
3-69024172-A-C		not specified	Uncertain significance (Jan 27, 2022)
3-69025568-G-A		not specified	Uncertain significance (May 03, 2023)
3-69025594-A-G		not specified	Uncertain significance (Aug 16, 2022)
3-69025676-T-C		not specified	Likely benign (Jan 03, 2024)
3-69025690-A-C		not specified	Uncertain significance (Sep 16, 2021)
3-69026027-A-C		not specified	Uncertain significance (Oct 26, 2022)
3-69026027-A-G		not specified	Uncertain significance (Jun 22, 2024)
3-69026039-C-T		not specified	Uncertain significance (May 28, 2024)
3-69026063-G-A		not specified	Uncertain significance (Oct 13, 2023)
3-69026094-G-A		not specified	Uncertain significance (Oct 29, 2021)
3-69027958-A-T		not specified	Uncertain significance (Mar 20, 2024)
3-69027962-T-C		not specified	Uncertain significance (Apr 05, 2023)
3-69028239-G-T		not specified	Uncertain significance (Feb 14, 2023)
3-69029853-C-A		not specified	Uncertain significance (Apr 10, 2023)
3-69029869-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-69029882-T-C		not specified	Uncertain significance (Jan 18, 2022)
3-69029890-T-C		not specified	Uncertain significance (Apr 22, 2022)
3-69029911-G-A		not specified	Uncertain significance (May 26, 2023)
3-69029928-C-G		not specified	Uncertain significance (Apr 22, 2022)
3-69029948-G-C		not specified	Uncertain significance (Aug 12, 2021)
3-69033586-G-A		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMF1	protein_coding	protein_coding	ENST00000398559	17	32507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000145	1.00	124759	0	34	124793	0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.417	517	544	0.950	0.0000270	7185
Missense in Polyphen		124	172.15	0.7203		2341
Synonymous	-1.22	212	191	1.11	0.00000922	2016
Loss of Function	4.54	19	55.5	0.342	0.00000300	710

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000414	0.000411
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000175	0.000167
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.000175	0.000167
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential coactivator of the androgen receptor. Mediates STAT3 degradation. May play critical roles in two RAB6-dependent retrograde transport processes: one from endosomes to the Golgi and the other from the Golgi to the ER. This protein binds the HIV-1 TATA element and inhibits transcriptional activation by the TATA-binding protein (TBP). {ECO:0000269|PubMed:10428808, ECO:0000269|PubMed:1409643, ECO:0000269|PubMed:15467733, ECO:0000269|PubMed:17698061}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;AndrogenReceptor;Coregulation of Androgen receptor activity;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.485
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.2

Haploinsufficiency Scores

• pHI: 0.439
• hipred: Y
• hipred_score: 0.548
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.627

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmf1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: acrosome assembly;positive regulation of cytokine production;regulation of transcription, DNA-templated;transcription by RNA polymerase II;spermatid nucleus differentiation;negative regulation of gene expression;flagellated sperm motility;luteinizing hormone secretion;Leydig cell differentiation;defense response to bacterium;negative regulation of apoptotic process;regulation of proteasomal protein catabolic process;cellular response to organic cyclic compound;positive regulation of testosterone secretion
• Cellular component: Golgi membrane;nucleus;endoplasmic reticulum;Golgi apparatus;cytosol
• Molecular function: DNA binding;transcription coregulator activity;protein binding