TFDP1

protein-coding

transcription factor Dp-1, the group of Transcription factor Dp family

Gene summary

This gene encodes a member of a family of transcription factors that heterodimerize with E2F proteins to enhance their DNA-binding activity and promote transcription from E2F target genes. The encoded protein functions as part of this complex to control the transcriptional activity of numerous genes involved in cell cycle progression from G1 to S phase. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 1, 15, and X.[provided by RefSeq, Jan 2009]

MANE transcript

NM_007111.5

Inheritance

—

ClinVar variants

U:49B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr13:113,584,721-113,641,473

External References & Databases

Ensembl (ENSG00000198176)

Transcript & Mutation Effects

hg38 • Region Span ~56.8 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 TFDP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007111.5. 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		2 clinvar	3
missense			41 clinvar	3 clinvar		44
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	49	3	2	54

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 141 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007111.5	RefSeq	NP_009042.1	11	MANE Select
ENST00000375370.10	Ensembl	ENSP00000364519.4	11	MANE Select
ENST00000408980.6	Ensembl	ENSP00000386145.2	8	Standard
ENST00000453989.2	Ensembl	ENSP00000401389.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TGF-beta signaling pathway - Homo sapiens (human)
Cell cycle - Homo sapiens (human)
Cell Cycle
Retinoblastoma (RB) in Cancer
regulation of p27 phosphorylation during cell cycle progression

Biological Process

regulation of transcription involved in G1/S transition of mitotic cell cycle
regulation of transcription by RNA polymerase II
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
cell population proliferation
epidermis development

Molecular Function

RNA polymerase II regulatory region sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
DNA-binding transcription factor activity
transcription coactivator activity

Cellular Component

nucleus
nucleoplasm
mitochondrion
cytosol
RNA polymerase II transcription factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375370
Coding exons: 11
Length: 56773
Individuals with no LoFs: 125745
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125748
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.28	159	263	0.604	0.0000165	2710
Missense (PolyPhen)		21	66.742	0.31464		806
Synonymous	1.08	100	115	0.872	0.00000883	781
Loss of Function	3.71	2	19.8	0.101	8.40e-7	239

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Can stimulate E2F-dependent transcription. Binds DNA cooperatively with E2F family members through the E2 recognition site, 5'-TTTC[CG]CGC-3', found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication (PubMed:8405995, PubMed:7739537). The E2F1:DP complex appears to mediate both cell proliferation and apoptosis. Blocks adipocyte differentiation by repressing CEBPA binding to its target gene promoters (PubMed:20176812). {ECO:0000269|PubMed:20176812, ECO:0000269|PubMed:7739537, ECO:0000269|PubMed:8405995}.;

Recessive Scores

pRec: 0.272

Intolerance Scores

LoFtool: 0.136
RVIS EVS: -1.02
RVIS percentile EVS: 7.94

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.976

Gene Damage Prediction

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