TMF1

protein-coding

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

Gene summary

Enables nuclear androgen receptor binding activity and transcription coactivator activity. Involved in androgen receptor signaling pathway and positive regulation of transcription by RNA polymerase II. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_007114.3

Inheritance

—

ClinVar variants

U:141B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr3:69,019,827-69,052,339

External References & Databases

Ensembl (ENSG00000144747)

Transcript & Mutation Effects

hg38 • Region Span ~32.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007114.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			133 clinvar	10 clinvar		143
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	141	11	0	152

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007114.3	RefSeq	NP_009045.2	17	MANE Select
ENST00000398559.7	Ensembl	ENSP00000381567.2	17	MANE Select
NM_001363879.1	RefSeq	NP_001350808.1	17	Standard
ENST00000488010.5	Ensembl	ENSP00000419330.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
AndrogenReceptor
Coregulation of Androgen receptor activity
Retrograde transport at the Trans-Golgi-Network

Biological Process

acrosome assembly
positive regulation of cytokine production
regulation of transcription, DNA-templated
transcription by RNA polymerase II
spermatid nucleus differentiation

Molecular Function

DNA binding
transcription coregulator activity
protein binding

Cellular Component

Golgi membrane
nucleus
endoplasmic reticulum
Golgi apparatus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398559
Coding exons: 17
Length: 32507
Individuals with no LoFs: 124759
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 124793
p: 0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.417	517	544	0.950	0.0000270	7185
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00033	0.00032	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00018	0.00017	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.485
RVIS EVS: -0.08
RVIS percentile EVS: 47.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.627

Gene Damage Prediction

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